diff --git a/Framework/Algorithms/src/GetAllEi.cpp b/Framework/Algorithms/src/GetAllEi.cpp
index 60418d5071ea437e50237e3f826e2d099efadc9e..2ba9d8bff8c4935ae69d7d8aa3eb1b2b7efa5590 100644
--- a/Framework/Algorithms/src/GetAllEi.cpp
+++ b/Framework/Algorithms/src/GetAllEi.cpp
@@ -754,7 +754,7 @@ bool refineEGuess(const MantidVec &eBins, const MantidVec &signal,
struct peakKeeper2 {
double left_rng;
double right_rng;
- peakKeeper2(){};
+ peakKeeper2() : left_rng(.0), right_rng(.0){};
peakKeeper2(double left, double right) : left_rng(left), right_rng(right) {}
};
}
@@ -985,6 +985,12 @@ GetAllEi::getAvrgLogValue(const API::MatrixWorkspace_sptr &inputWS,
auto pTimeSeries =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(pIProperty);
+ if (!pTimeSeries) {
+ throw std::runtime_error(
+ "Could not retrieve a time series property for the property name " +
+ propertyName);
+ }
+
if (splitter.size() == 0) {
auto TimeStart = inputWS->run().startTime();
auto TimeEnd = inputWS->run().endTime();
diff --git a/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp b/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
index 8970268ec6e453b2326086689c3977de04cf60a3..754509ce3c9bb695d51fcf4ecd33c927b2509ffd 100644
--- a/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
+++ b/Framework/Algorithms/src/IdentifyNoisyDetectors.cpp
@@ -137,6 +137,11 @@ void IdentifyNoisyDetectors::getStdDev(MatrixWorkspace_sptr valid,
}
}
+ if (0 == count) {
+ // all values are zero, no need to loop
+ return;
+ }
+
mean = mean / count;
double stddev = sqrt((mean2 / count) - std::pow(mean, 2));
diff --git a/Framework/Algorithms/src/ResizeRectangularDetector.cpp b/Framework/Algorithms/src/ResizeRectangularDetector.cpp
index 564cb8d85ce64d5dbc79efe15edefc9ad619458e..9378f6e68407b8b0936036727b89c9c895ab4cb9 100644
--- a/Framework/Algorithms/src/ResizeRectangularDetector.cpp
+++ b/Framework/Algorithms/src/ResizeRectangularDetector.cpp
@@ -74,8 +74,21 @@ void ResizeRectangularDetector::exec() {
Instrument_sptr inst;
if (inputW) {
inst = boost::const_pointer_cast<Instrument>(inputW->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "MatrixWorkspace provided as input");
+
} else if (inputP) {
inst = boost::const_pointer_cast<Instrument>(inputP->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "PeaksWorkspace provided as input");
+ } else {
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "workspace and it does not seem to be valid as "
+ "input (must be either MatrixWorkspace or "
+ "PeaksWorkspace");
}
std::string ComponentName = getPropertyValue("ComponentName");
diff --git a/Framework/Crystal/src/IntegratePeakTimeSlices.cpp b/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
index 9828bea2f54bfa54db588459eca4c19b2d772842..92558503c80fd9fed7c50e719f19c17ddd805321 100644
--- a/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
+++ b/Framework/Crystal/src/IntegratePeakTimeSlices.cpp
@@ -595,7 +595,8 @@ void IntegratePeakTimeSlices::exec() {
lastRow = (int)(params[i] + .5);
i = find("Mcol", names);
- lastCol = (int)(params[i] + .5);
+ if (i >= 0)
+ lastCol = (int)(params[i] + .5);
prog.report();
} else if (dir > 0)
diff --git a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
index 87801460543315e7aaccd4501e43e74facf27e8f..71021ad4567b7bbed8fc34f07954ebad74a60fa3 100644
--- a/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
+++ b/Framework/CurveFitting/src/Algorithms/FitPowderDiffPeaks.cpp
@@ -2081,7 +2081,8 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
bool fitgood = doFitNPeaksSimple(dataws, wsindex, peaksfunc, peakfuncs,
"Levenberg-MarquardtMD", 1000, chi2);
- evergood = evergood || fitgood;
+ // not required. before loop starts, evergood=fitgood WITH fitgood==true
+ // evergood = evergood || fitgood;
// c) Process the result
if (!fitgood)
@@ -2098,7 +2099,8 @@ bool FitPowderDiffPeaks::doFitMultiplePeaks(
storeFunctionParameters(peaksfunc, peaksfuncparams);
fitgood = doFitNPeaksSimple(dataws, wsindex, peaksfunc, peakfuncs,
"Levenberg-MarquardtMD", 1000, chi2);
- evergood = evergood || fitgood;
+ // not required. before, evergood=fitgood WITH fitgood==true
+ // evergood = evergood || fitgood;
if (!fitgood)
restoreFunctionParameters(peaksfunc, peaksfuncparams);
diff --git a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
index a19fa51061060d39206dd760f8a1d8db453d9fb0..c9ba83eb4f203689aa8651bdf57762652a205b0c 100644
--- a/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
+++ b/Framework/CurveFitting/src/Algorithms/SplineBackground.cpp
@@ -66,8 +66,8 @@ void SplineBackground::exec() {
bool isMasked = inWS->hasMaskedBins(spec);
std::vector<int> masked(Y.size());
if (isMasked) {
- for (auto it = inWS->maskedBins(spec).begin();
- it != inWS->maskedBins(spec).end(); ++it)
+ auto maskedBins = inWS->maskedBins(spec);
+ for (auto it = maskedBins.begin(); it != maskedBins.end(); ++it)
masked[it->first] = 1;
n -= static_cast<int>(inWS->maskedBins(spec).size());
}
diff --git a/Framework/DataHandling/inc/MantidDataHandling/LoadIsawDetCal.h b/Framework/DataHandling/inc/MantidDataHandling/LoadIsawDetCal.h
index 7c789334c19d420896d82e3c754599dfc9ef10f7..65dce045094d0c534654bed7749e496ba0c94b40 100644
--- a/Framework/DataHandling/inc/MantidDataHandling/LoadIsawDetCal.h
+++ b/Framework/DataHandling/inc/MantidDataHandling/LoadIsawDetCal.h
@@ -5,6 +5,8 @@
// Includes
//----------------------------------------------------------------------
#include "MantidAPI/Algorithm.h"
+#include "MantidGeometry/Instrument.h"
+
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_multifit_nlin.h>
#include <gsl/gsl_multimin.h>
@@ -70,6 +72,8 @@ private:
// Overridden Algorithm methods
void init();
void exec();
+
+ Geometry::Instrument_sptr getCheckInst(API::Workspace_sptr ws);
};
} // namespace DataHandling
diff --git a/Framework/DataHandling/src/GroupDetectors2.cpp b/Framework/DataHandling/src/GroupDetectors2.cpp
index 7567cc8e6da22794430ce706cb97c7f5d4c1aeca..8e9b3d0d0927e0d5a746f0cf5c994dfbc6a40d3c 100644
--- a/Framework/DataHandling/src/GroupDetectors2.cpp
+++ b/Framework/DataHandling/src/GroupDetectors2.cpp
@@ -353,8 +353,9 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
}
// check we don't have an index that is too high for the workspace
size_t maxIn = static_cast<size_t>(workspace->getNumberHistograms() - 1);
- auto it = m_GroupSpecInds[0].begin();
- for (; it != m_GroupSpecInds[0].end(); ++it) {
+ auto indices0 = m_GroupSpecInds[0];
+ auto it = indices0.begin();
+ for (; it != indices0.end(); ++it) {
if (*it > maxIn) {
g_log.error() << "Spectra index " << *it
<< " doesn't exist in the input workspace, the highest "
@@ -375,8 +376,9 @@ void GroupDetectors2::getGroups(API::MatrixWorkspace_const_sptr workspace,
// up date unUsedSpec, this is used to find duplicates and when the user has
// set KeepUngroupedSpectra
- auto index = m_GroupSpecInds[0].begin();
- for (; index != m_GroupSpecInds[0].end();
+ auto indices0 = m_GroupSpecInds[0];
+ auto index = indices0.begin();
+ for (; index != indices0.end();
++index) { // the vector<int> m_GroupSpecInds[0] must not index contain
// numbers that don't exist in the workspaace
if (unUsedSpec[*index] != USED) {
diff --git a/Framework/DataHandling/src/LoadIsawDetCal.cpp b/Framework/DataHandling/src/LoadIsawDetCal.cpp
index 2fc3168b716430b093a5fd2da80f0ef2f1aa17fa..02828ea742261cedb9b45d808a59049f4846d0fc 100644
--- a/Framework/DataHandling/src/LoadIsawDetCal.cpp
+++ b/Framework/DataHandling/src/LoadIsawDetCal.cpp
@@ -40,52 +40,6 @@ LoadIsawDetCal::LoadIsawDetCal() : API::Algorithm() {}
/// Destructor
LoadIsawDetCal::~LoadIsawDetCal() {}
-/**
- * The intensity function calculates the intensity as a function of detector
- * position and angles
- * @param x :: The shift along the X-axis
- * @param y :: The shift along the Y-axis
- * @param z :: The shift along the Z-axis
- * @param detname :: The detector name
- * @param ws :: The workspace
- */
-
-void LoadIsawDetCal::center(double x, double y, double z, std::string detname,
- API::Workspace_sptr ws) {
- MatrixWorkspace_sptr inputW =
- boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
- PeaksWorkspace_sptr inputP = boost::dynamic_pointer_cast<PeaksWorkspace>(ws);
-
- // Get some stuff from the input workspace
- Instrument_sptr inst;
- if (inputW) {
- inst = boost::const_pointer_cast<Instrument>(inputW->getInstrument());
- } else if (inputP) {
- inst = boost::const_pointer_cast<Instrument>(inputP->getInstrument());
- }
-
- IComponent_const_sptr comp = inst->getComponentByName(detname);
- if (comp == 0) {
- std::ostringstream mess;
- mess << "Component with name " << detname << " was not found.";
- g_log.error(mess.str());
- throw std::runtime_error(mess.str());
- }
-
- // Do the move
- using namespace Geometry::ComponentHelper;
- TransformType positionType = Absolute;
- if (inputW) {
- Geometry::ParameterMap &pmap = inputW->instrumentParameters();
- Geometry::ComponentHelper::moveComponent(*comp, pmap, V3D(x, y, z),
- positionType);
- } else if (inputP) {
- Geometry::ParameterMap &pmap = inputP->instrumentParameters();
- Geometry::ComponentHelper::moveComponent(*comp, pmap, V3D(x, y, z),
- positionType);
- }
-}
-
/** Initialisation method
*/
void LoadIsawDetCal::init() {
@@ -118,13 +72,7 @@ void LoadIsawDetCal::exec() {
boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
PeaksWorkspace_sptr inputP = boost::dynamic_pointer_cast<PeaksWorkspace>(ws);
- // Get some stuff from the input workspace
- Instrument_sptr inst;
- if (inputW) {
- inst = boost::const_pointer_cast<Instrument>(inputW->getInstrument());
- } else if (inputP) {
- inst = boost::const_pointer_cast<Instrument>(inputP->getInstrument());
- }
+ Instrument_sptr inst = getCheckInst(ws);
std::string instname = inst->getName();
@@ -437,5 +385,82 @@ void LoadIsawDetCal::exec() {
return;
}
+/**
+ * The intensity function calculates the intensity as a function of detector
+ * position and angles
+ * @param x :: The shift along the X-axis
+ * @param y :: The shift along the Y-axis
+ * @param z :: The shift along the Z-axis
+ * @param detname :: The detector name
+ * @param ws :: The workspace
+ */
+
+void LoadIsawDetCal::center(double x, double y, double z, std::string detname,
+ API::Workspace_sptr ws) {
+
+ Instrument_sptr inst = getCheckInst(ws);
+
+ IComponent_const_sptr comp = inst->getComponentByName(detname);
+ if (comp == 0) {
+ std::ostringstream mess;
+ mess << "Component with name " << detname << " was not found.";
+ g_log.error(mess.str());
+ throw std::runtime_error(mess.str());
+ }
+
+ // Do the move
+ using namespace Geometry::ComponentHelper;
+ TransformType positionType = Absolute;
+ MatrixWorkspace_sptr inputW =
+ boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
+ PeaksWorkspace_sptr inputP = boost::dynamic_pointer_cast<PeaksWorkspace>(ws);
+ if (inputW) {
+ Geometry::ParameterMap &pmap = inputW->instrumentParameters();
+ Geometry::ComponentHelper::moveComponent(*comp, pmap, V3D(x, y, z),
+ positionType);
+ } else if (inputP) {
+ Geometry::ParameterMap &pmap = inputP->instrumentParameters();
+ Geometry::ComponentHelper::moveComponent(*comp, pmap, V3D(x, y, z),
+ positionType);
+ }
+}
+
+/**
+ * Gets the instrument of the workspace, checking that the workspace
+ * and the instrument are as expected.
+ *
+ * @param ws workspace (expected Matrix or Peaks Workspace)
+ *
+ * @throw std::runtime_error if there's any problem with the workspace or it is
+ * not possible to get an instrument object from it
+ */
+Instrument_sptr LoadIsawDetCal::getCheckInst(API::Workspace_sptr ws) {
+ MatrixWorkspace_sptr inputW =
+ boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
+ PeaksWorkspace_sptr inputP = boost::dynamic_pointer_cast<PeaksWorkspace>(ws);
+
+ // Get some stuff from the input workspace
+ Instrument_sptr inst;
+ if (inputW) {
+ inst = boost::const_pointer_cast<Instrument>(inputW->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "MatrixWorkspace provided as input");
+ } else if (inputP) {
+ inst = boost::const_pointer_cast<Instrument>(inputP->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "PeaksWorkspace provided as input");
+ } else {
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "workspace which does not seem to be valid as "
+ "input (must be either MatrixWorkspace or "
+ "PeaksWorkspace");
+ }
+
+ return inst;
+}
+
} // namespace Algorithm
} // namespace Mantid
diff --git a/Framework/DataHandling/src/RotateInstrumentComponent.cpp b/Framework/DataHandling/src/RotateInstrumentComponent.cpp
index 8cb5b36d8803563a9ccf23cb0b265edaaca362dd..adf61ef3c061e495d3f8ea629a531897fccae69a 100644
--- a/Framework/DataHandling/src/RotateInstrumentComponent.cpp
+++ b/Framework/DataHandling/src/RotateInstrumentComponent.cpp
@@ -61,8 +61,20 @@ void RotateInstrumentComponent::exec() {
Instrument_sptr inst;
if (inputW) {
inst = boost::const_pointer_cast<Instrument>(inputW->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "MatrixWorkspace provided as input");
} else if (inputP) {
inst = boost::const_pointer_cast<Instrument>(inputP->getInstrument());
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "PeaksWorkspace provided as input");
+ } else {
+ if (!inst)
+ throw std::runtime_error("Could not get a valid instrument from the "
+ "workspace and it does not seem to be valid as "
+ "input (must be either MatrixWorkspace or "
+ "PeaksWorkspace");
}
const std::string ComponentName = getProperty("ComponentName");
diff --git a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
index 4de121711232aa6c6a24fd477c7118097ca62778..779c3a641cc521b38ff68c8af3193c88f37c4e64 100644
--- a/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
+++ b/Framework/DataObjects/inc/MantidDataObjects/MDGridBox.tcc
@@ -1462,8 +1462,8 @@ TMDE(void MDGridBox)::integrateCylinder(
// Distance from center to the peak integration center
coord_t out[nd];
radiusTransform.apply(boxCenter, out);
- if (out[0] < std::sqrt(diagonalSquared * 0.72 + radius * radius) &&
- (nd >= 1 &&
+ if ((nd >= 1) && out[0] < std::sqrt(diagonalSquared * 0.72 + radius * radius) &&
+ (nd >= 2 &&
std::fabs(out[1]) <
std::sqrt(diagonalSquared * 0.72 + 0.25 * length * length))) {
// If the center is closer than the size of the box, then it MIGHT be
diff --git a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
index f4c9afef815111745fea386715ae9a79b4d531ea..547f95e5a70e134f2a68d069a107be1b9c194574 100644
--- a/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
+++ b/Framework/Geometry/src/Instrument/InstrumentDefinitionParser.cpp
@@ -1502,8 +1502,16 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
if (pE->hasAttribute("step"))
increment = atoi((pE->getAttribute("step")).c_str());
+ if (0 == increment) {
+ std::stringstream ss;
+ ss << "The step element cannot be zero, got start: " << startID
+ << ", end: " << endID << ", step: " << increment;
+ throw Kernel::Exception::InstrumentDefinitionError(ss.str(), filename);
+ }
+
// check the start end and increment values are sensible
- if (((endID - startID) / increment) < 0) {
+ int steps = (endID - startID) / increment;
+ if (steps < 0) {
std::stringstream ss;
ss << "The start, end, and step elements do not allow a single id in the "
"idlist entry - ";
@@ -1513,7 +1521,7 @@ void InstrumentDefinitionParser::populateIdList(Poco::XML::Element *pE,
throw Kernel::Exception::InstrumentDefinitionError(ss.str(), filename);
}
- idList.vec.reserve((endID - startID) / increment);
+ idList.vec.reserve(steps);
for (int i = startID; i != endID + increment; i += increment) {
idList.vec.push_back(i);
}
diff --git a/Framework/ICat/src/GSoap/stdsoap2.cpp b/Framework/ICat/src/GSoap/stdsoap2.cpp
index 252bc7ae6514f1f8380bd35f9c89fcc5e46abd54..d351d6dcbe205759e64022794e4a7dcbbd5662d5 100644
--- a/Framework/ICat/src/GSoap/stdsoap2.cpp
+++ b/Framework/ICat/src/GSoap/stdsoap2.cpp
@@ -312,9 +312,21 @@ static const char *soap_strerror(struct soap *);
ioctl(fd, 0 /*FIONBIO*/, &nonblocking); \
}
#else
-#define SOAP_SOCKBLOCK(fd) fcntl(fd, F_SETFL, fcntl(fd, F_GETFL) & ~O_NONBLOCK);
+#define SOAP_SOCKBLOCK(fd) \
+ { \
+ int retv = fcntl(fd, F_SETFL, fcntl(fd, F_GETFL) & ~O_NONBLOCK); \
+ if (retv < 0) { \
+ DBGLOG(TEST, SOAP_MESSAGE(fdebug, "SOAP_SOCKBLOCK (fcntl) failed\n")); \
+ } \
+ }
#define SOAP_SOCKNONBLOCK(fd) \
- fcntl(fd, F_SETFL, fcntl(fd, F_GETFL) | O_NONBLOCK);
+ { \
+ int retv = fcntl(fd, F_SETFL, fcntl(fd, F_GETFL) | O_NONBLOCK); \
+ if (retv < 0) { \
+ DBGLOG(TEST, \
+ SOAP_MESSAGE(fdebug, "SOAP_SOCNONKBLOCK (fcntl) failed\n")); \
+ } \
+ }
#endif
#endif
@@ -2348,7 +2360,8 @@ int SOAP_FMAC2 soap_resolve(struct soap *soap) {
} else if (*ip->id == '#') {
DBGLOG(TEST,
SOAP_MESSAGE(fdebug, "Missing data for id='%s'\n", ip->id));
- strncpy(soap->id, ip->id + 1, sizeof(soap->id));
+ strncpy(soap->id, ip->id + 1, sizeof(soap->id) - 1);
+ soap->id[sizeof(soap->id) - 1] = '\0';
return soap->error = SOAP_MISSING_ID;
}
}
@@ -3206,9 +3219,10 @@ const char *SOAP_FMAC2 soap_ssl_error(struct soap *soap, int ret) {
#ifdef WITH_OPENSSL
int err = SSL_get_error(soap->ssl, ret);
const char *msg = soap_code_str(h_ssl_error_codes, err);
- if (msg)
- strncpy(soap->msgbuf, msg, sizeof(soap->msgbuf));
- else
+ if (msg) {
+ strncpy(soap->msgbuf, msg, sizeof(soap->msgbuf) - 1);
+ soap->msgbuf[sizeof(soap->msgbuf) - 1] = '\0';
+ } else
return ERR_error_string(err, soap->msgbuf);
if (ERR_peek_error()) {
unsigned long r;
@@ -3715,10 +3729,11 @@ int SOAP_FMAC2 soap_ssl_accept(struct soap *soap) {
}
}
#endif
- if (soap->recv_timeout || soap->send_timeout)
+ if (soap->recv_timeout || soap->send_timeout) {
SOAP_SOCKNONBLOCK(sk)
- else
+ } else {
SOAP_SOCKBLOCK(sk)
+ }
soap->imode |= SOAP_ENC_SSL;
soap->omode |= SOAP_ENC_SSL;
return SOAP_OK;
@@ -4615,10 +4630,11 @@ again:
return SOAP_INVALID_SOCKET;
#endif
}
- if (soap->recv_timeout || soap->send_timeout)
+ if (soap->recv_timeout || soap->send_timeout) {
SOAP_SOCKNONBLOCK(sk)
- else
+ } else {
SOAP_SOCKBLOCK(sk)
+ }
return sk;
}
#endif
@@ -5169,10 +5185,11 @@ soap_accept(struct soap *soap) {
}
}
}
- if (soap->accept_timeout)
+ if (soap->accept_timeout) {
SOAP_SOCKNONBLOCK(soap->master)
- else
+ } else {
SOAP_SOCKBLOCK(soap->master)
+ }
soap->socket =
soap->faccept(soap, soap->master, (struct sockaddr *)&soap->peer, &n);
soap->peerlen = (size_t)n;
@@ -5266,10 +5283,12 @@ soap_accept(struct soap *soap) {
#endif
soap->keep_alive =
(((soap->imode | soap->omode) & SOAP_IO_KEEPALIVE) != 0);
- if (soap->send_timeout || soap->recv_timeout)
+
+ if (soap->send_timeout || soap->recv_timeout) {
SOAP_SOCKNONBLOCK(soap->socket)
- else
+ } else {
SOAP_SOCKBLOCK(soap->socket)
+ }
return soap->socket;
}
err = soap_socket_errno(soap->socket);
@@ -6049,7 +6068,10 @@ static int http_post(struct soap *soap, const char *endpoint, const char *host,
sprintf(soap->tmpbuf, "[%s]", host); /* RFC 2732 */
else
#endif
- strncpy(soap->tmpbuf, host, sizeof(soap->tmpbuf));
+ {
+ strncpy(soap->tmpbuf, host, sizeof(soap->tmpbuf) - 1);
+ soap->tmpbuf[sizeof(soap->tmpbuf) - 1] = '\0';
+ }
}
if ((err = soap->fposthdr(soap, "Host", soap->tmpbuf)))
return err;
@@ -8161,7 +8183,8 @@ void *SOAP_FMAC2 soap_id_lookup(struct soap *soap, const char *id, void **p,
"Resolved href='%s' type=%d location=%p (%u bytes)\n",
id, t, ip->ptr, (unsigned int)n));
if (ip->type != t) {
- strncpy(soap->id, id, sizeof(soap->id));
+ strncpy(soap->id, id, sizeof(soap->id) - 1);
+ soap->id[sizeof(soap->id) - 1] = '\0';
soap->error = SOAP_HREF;
DBGLOG(TEST,
SOAP_MESSAGE(
@@ -8265,7 +8288,8 @@ void *SOAP_FMAC2 soap_id_forward(struct soap *soap, const char *href, void *p,
"size=%lu level=%u got type=%d size=%lu\n",
href, ip->type, (unsigned long)ip->size, k, st,
(unsigned long)n));
- strncpy(soap->id, href, sizeof(soap->id));
+ strncpy(soap->id, href, sizeof(soap->id) - 1);
+ soap->id[sizeof(soap->id) - 1] = '\0';
soap->error = SOAP_HREF;
return NULL;
}
@@ -8357,12 +8381,14 @@ soap_id_enter(struct soap *soap, const char *id, void *p, int t, size_t n,
"size=%lu level=%u got type=%d size=%lu\n",
id, ip->type, (unsigned long)ip->size, k, t,
(unsigned long)n));
- strncpy(soap->id, id, sizeof(soap->id));
+ strncpy(soap->id, id, sizeof(soap->id) - 1);
+ soap->id[sizeof(soap->id) - 1] = '\0';
soap->error = SOAP_HREF;
return NULL;
} else if (ip->ptr) {
DBGLOG(TEST, SOAP_MESSAGE(fdebug, "Multiply defined id='%s'\n", id));
- strncpy(soap->id, id, sizeof(soap->id));
+ strncpy(soap->id, id, sizeof(soap->id) - 1);
+ soap->id[sizeof(soap->id) - 1] = '\0';
soap->error = SOAP_DUPLICATE_ID;
return NULL;
} else {
@@ -16431,14 +16457,48 @@ int SOAP_FMAC2 soap_send_fault(struct soap *soap) {
soap_serializefault(soap);
soap_begin_count(soap);
if (soap->mode & SOAP_IO_LENGTH) {
- soap_envelope_begin_out(soap);
- soap_putheader(soap);
- soap_body_begin_out(soap);
- soap_putfault(soap);
- soap_body_end_out(soap);
- soap_envelope_end_out(soap);
+ int retv = soap_envelope_begin_out(soap);
+ if (retv < 0) {
+ DBGLOG(
+ TEST,
+ SOAP_MESSAGE(
+ fdebug,
+ "soap_envelope_begin_out() failed in soap_send_fault()\n"));
+ }
+ retv = soap_putheader(soap);
+ if (retv < 0) {
+ DBGLOG(TEST,
+ SOAP_MESSAGE(
+ fdebug, "soap_putheader() failed in soap_send_fault()\n"));
+ }
+ retv = soap_body_begin_out(soap);
+ if (retv < 0) {
+ DBGLOG(TEST,
+ SOAP_MESSAGE(
+ fdebug,
+ "soap_body_begin_out() failed in soap_send_fault()\n"));
+ }
+ retv = soap_putfault(soap);
+ if (retv < 0) {
+ DBGLOG(TEST,
+ SOAP_MESSAGE(fdebug,
+ "soap_putfault() failed in soap_send_fault()\n"));
+ }
+ retv = soap_body_end_out(soap);
+ if (retv < 0) {
+ DBGLOG(
+ TEST,
+ SOAP_MESSAGE(
+ fdebug, "soap_body_end_out() failed in soap_send_fault()\n"));
+ }
+ retv = soap_envelope_end_out(soap);
+ }
+ int retv = soap_end_count(soap);
+ if (retv < 0) {
+ DBGLOG(TEST,
+ SOAP_MESSAGE(fdebug,
+ "soap_end_count() failed in soap_send_fault()\n"));
}
- soap_end_count(soap);
if (soap_response(soap, status) || soap_envelope_begin_out(soap) ||
soap_putheader(soap) || soap_body_begin_out(soap) ||
soap_putfault(soap) || soap_body_end_out(soap) ||
@@ -16500,7 +16560,11 @@ int SOAP_FMAC2 soap_recv_fault(struct soap *soap, int check) {
if (!soap_body_end_in(soap))
soap_envelope_end_in(soap);
}
- soap_end_recv(soap);
+ int recvsts = soap_end_recv(soap);
+ if (recvsts < 0) {
+ DBGLOG(TEST, SOAP_MESSAGE(fdebug, "soap_end_recv() failed with status %d\n",
+ status));
+ }
soap->error = status;
return soap_closesock(soap);
}
@@ -16531,9 +16595,16 @@ int SOAP_FMAC2 soap_send_empty_response(struct soap *soap, int httpstatuscode) {
SOAP_FMAC1
int SOAP_FMAC2 soap_recv_empty_response(struct soap *soap) {
if (!(soap->omode & SOAP_IO_UDP)) {
- if (!soap_begin_recv(soap))
+ if (!soap_begin_recv(soap)) {
soap_end_recv(soap);
- else if (soap->error == SOAP_NO_DATA || soap->error == 202)
+ int recvsts = soap_end_recv(soap);
+ if (recvsts < 0) {
+ DBGLOG(TEST,
+ SOAP_MESSAGE(
+ fdebug,
+ "soap_end_recv() failed in soap_recv_empty_response()\n"));
+ }
+ } else if (soap->error == SOAP_NO_DATA || soap->error == 202)
soap->error = SOAP_OK;
}
return soap_closesock(soap);
diff --git a/Framework/Kernel/src/DateValidator.cpp b/Framework/Kernel/src/DateValidator.cpp
index 5362fb247e217211a577736781841c1057ccacfe..4f7eee94a2965d71a42716a384035b05ade82914 100644
--- a/Framework/Kernel/src/DateValidator.cpp
+++ b/Framework/Kernel/src/DateValidator.cpp
@@ -30,6 +30,7 @@ struct tm getTimeValue(const std::string &sDate, std::string &error) {
timeinfo.tm_isdst = -1;
#ifndef _WIN32
timeinfo.tm_gmtoff = 0;
+ timeinfo.tm_zone = 0;
#endif
std::basic_string<char>::size_type index, off = 0;
diff --git a/Framework/Kernel/src/VectorHelper.cpp b/Framework/Kernel/src/VectorHelper.cpp
index 52144d225aa4f454563c018cefb3c214ad817445..8764accf4f6cab5eefa4949cb3e9d311c35507aa 100644
--- a/Framework/Kernel/src/VectorHelper.cpp
+++ b/Framework/Kernel/src/VectorHelper.cpp
@@ -533,6 +533,7 @@ void linearlyInterpolateY(const std::vector<double> &x, std::vector<double> &y,
step++;
}
}
+
namespace {
/** internal function converted from Lambda to identify interval around
* specified point and run average around this point
@@ -551,7 +552,7 @@ double runAverage(size_t index, size_t startIndex, size_t endIndex,
std::vector<double> const *const binBndrs) {
size_t iStart, iEnd;
- double weight0(0), weight1(0), start, end;
+ double weight0(0), weight1(0), start(0.0), end(0.0);
//
if (binBndrs) {
// identify initial and final bins to
@@ -607,12 +608,21 @@ double runAverage(size_t index, size_t startIndex, size_t endIndex,
if (iEnd != endIndex)
avrg += input[iEnd] * weight1;
- return avrg / (end - start);
+ double div = end - start;
+ if (.0 == div)
+ return 0;
+ else
+ return avrg / (end - start);
} else {
- return avrg / double(ic);
+ if (0 == ic) {
+ return 0;
+ } else {
+ return avrg / double(ic);
+ }
}
}
}
+
/** Basic running average of input vector within specified range, considering
* variable bin-boundaries if such boundaries are provided.
* The algorithm performs trapezium integration, so some peak shift
@@ -683,11 +693,11 @@ void smoothInRange(const std::vector<double> &input,
output[i - startIndex] =
runAverage(i, startIndex, endIndex, halfWidth, input, binBndrs) *
binSize;
- if (outBins) {
+ if (outBins && binBndrs) {
outBins->operator[](i - startIndex) = binBndrs->operator[](i);
}
}
- if (outBins) {
+ if (outBins && binBndrs) {
outBins->operator[](endIndex - startIndex) = binBndrs->operator[](endIndex);
}
}
diff --git a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
index 5bb6cc662e53abe742bfb355143983a89573ce5d..22507befa430a047f4f1cb757bc943df762b53df 100644
--- a/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
+++ b/Framework/MDAlgorithms/src/ConvertCWSDExpToMomentum.cpp
@@ -415,6 +415,13 @@ void ConvertCWSDExpToMomentum::convertSpiceMatrixToMomentumMDEvents(
}
expinfo->mutableRun().setGoniometer(dataws->run().getGoniometer(), false);
expinfo->mutableRun().addProperty("run_number", runnumber);
+ // Add all the other propertys from original data workspace
+ const std::vector<Kernel::Property *> vec_property =
+ dataws->run().getProperties();
+ for (size_t i = 0; i < vec_property.size(); ++i) {
+ expinfo->mutableRun().addProperty(vec_property[i]->clone());
+ }
+
m_outputWS->addExperimentInfo(expinfo);
return;
diff --git a/Framework/MDAlgorithms/test/CompactMDTest.h b/Framework/MDAlgorithms/test/CompactMDTest.h
index 2dc03cfe8ee693a245bdff1552c31d894a13dc68..c902a63bd606528350418ca3664b634d0314e4bd 100644
--- a/Framework/MDAlgorithms/test/CompactMDTest.h
+++ b/Framework/MDAlgorithms/test/CompactMDTest.h
@@ -34,9 +34,9 @@ public:
* Input structure:
*------------------
* -------------
- * | |///| |
- * -------------
- * -3-2-1 0 1 2 3
+ * | | |///| | |
+ * ---------------------
+ * -5-4-3 2-1 0 1 2 3 4 5
*---------------------------
* Expected output structure:
*----------------------------
@@ -51,13 +51,13 @@ public:
const size_t numDims = 1;
const double signal = 0.0;
const double errorSquared = 1.3;
- size_t numBins[static_cast<int>(numDims)] = {3};
- Mantid::coord_t min[static_cast<int>(numDims)] = {-3};
- Mantid::coord_t max[static_cast<int>(numDims)] = {3};
+ size_t numBins[static_cast<int>(numDims)] = {5};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-5};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {5};
const std::string name("test");
auto inWS = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
numDims, signal, errorSquared, numBins, min, max, name);
- inWS->setSignalAt(1, 1.0); // set middle bin signal to one
+ inWS->setSignalAt(2, 1.0); // set middle bin signal to one
CompactMD alg;
alg.setChild(true);
alg.setRethrows(true);
@@ -258,17 +258,22 @@ public:
const size_t numDims = 4;
const double signal = 0.0;
const double errorSquared = 1.2;
- size_t numBins[static_cast<int>(numDims)] = {3, 3, 3, 3};
- Mantid::coord_t min[static_cast<int>(numDims)] = {-3, -3, -3, -3};
- Mantid::coord_t max[static_cast<int>(numDims)] = {3, 3, 3, 3};
+ size_t numBins[static_cast<int>(numDims)] = {10, 20, 10, 20};
+ Mantid::coord_t min[static_cast<int>(numDims)] = {-5, -10, -5, -10};
+ Mantid::coord_t max[static_cast<int>(numDims)] = {5, 10, 5, 10};
const std::string name("test");
m_ws = MDEventsTestHelper::makeFakeMDHistoWorkspaceGeneral(
numDims, signal, errorSquared, numBins, min, max, name);
+ // setting signals like this for variety
+ auto iter = m_ws->createIterator();
+ do {
+ auto index = iter->getLinearIndex();
+ if (index % 2 == 0) {
+ m_ws->setSignalAt(index, 1.0);
+ }
+ } while (iter->next());
}
void test_execute_4d() {
- m_ws->setSignalAt(0, 1.0);
- m_ws->setSignalAt(5, 1.2);
- m_ws->setSignalAt(1, 2.3);
CompactMD alg;
alg.setChild(true);
alg.setRethrows(true);
diff --git a/Framework/Properties/Mantid.properties.template b/Framework/Properties/Mantid.properties.template
index 27e669d1d7ff7c2297397b120797a006c97aa4b6..9b160ba84bb9860cdd4b2237dc08e7576198f65b 100644
--- a/Framework/Properties/Mantid.properties.template
+++ b/Framework/Properties/Mantid.properties.template
@@ -16,7 +16,7 @@ default.facility = ISIS
default.instrument =
# Set of PyQt interfaces to add to the Interfaces menu, separated by a space. Interfaces are seperated from their respective categories by a "/".
-mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py
+mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py Diffraction/HFIR_4Circle_Reduction.py
mantidqt.python_interfaces_directory = @MANTID_ROOT@/scripts
diff --git a/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py b/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py
new file mode 100644
index 0000000000000000000000000000000000000000..a6964b3768e7acd5a4056f52cbfb721c8c95ef06
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/ComputeCalibrationCoefVan.py
@@ -0,0 +1,168 @@
+from mantid.api import PythonAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty, Progress, InstrumentValidator
+from mantid.kernel import Direction
+import numpy as np
+from scipy import integrate
+import scipy as sp
+import mlzutils
+
+
+class ComputeCalibrationCoefVan(PythonAlgorithm):
+ """ Calculate coefficients to normalize by Vanadium and correct Debye Waller factor
+ """
+ def __init__(self):
+ """
+ Init
+ """
+ PythonAlgorithm.__init__(self)
+ self.vanaws = None
+ self.defaultT = 293.0 # K, default temperature if not given
+ self.Mvan = 50.942 # [g/mol], Vanadium molar mass
+ self.DebyeT = 389.0 # K, Debye temperature for Vanadium
+
+ def category(self):
+ """ Return category
+ """
+ return "PythonAlgorithms;CorrectionFunctions\\EfficiencyCorrections"
+
+ def name(self):
+ """ Return summary
+ """
+ return "ComputeCalibrationCoefVan"
+
+ def summary(self):
+ return "Calculate coefficients for detector efficiency correction using the Vanadium data."
+
+ def PyInit(self):
+ """ Declare properties
+ """
+ self.declareProperty(MatrixWorkspaceProperty("VanadiumWorkspace", "", direction=Direction.Input,
+ validator=InstrumentValidator()),
+ "Input Vanadium workspace")
+ self.declareProperty(MatrixWorkspaceProperty("OutputWorkspace", "", direction=Direction.Output),
+ "Name the workspace that will contain the calibration coefficients")
+ return
+
+ def validateInputs(self):
+ issues = dict()
+ inws = self.getProperty("VanadiumWorkspace").value
+ run = inws.getRun()
+
+ if not run.hasProperty('wavelength'):
+ issues['VanadiumWorkspace'] = "Input workspace must have wavelength sample log."
+ else:
+ try:
+ float(run.getProperty('wavelength').value)
+ except ValueError:
+ issues['VanadiumWorkspace'] = "Invalid value for wavelength sample log. Wavelength must be a number."
+
+ return issues
+
+ def get_temperature(self):
+ """
+ tries to get temperature from the sample logs
+ in the case of fail, default value is returned
+ """
+ run = self.vanaws.getRun()
+ if not run.hasProperty('temperature'):
+ self.log().warning("Temperature sample log is not present in " + self.vanaws.getName() +
+ " T=293K is assumed for Debye-Waller factor.")
+ return self.defaultT
+ try:
+ temperature = float(run.getProperty('temperature').value)
+ except ValueError, err:
+ self.log().warning("Error of getting temperature: " + err +
+ " T=293K is assumed for Debye-Waller factor.")
+ return self.defaultT
+
+ return temperature
+
+ def PyExec(self):
+ """ Main execution body
+ """
+ self.vanaws = self.getProperty("VanadiumWorkspace").value # returns workspace instance
+ outws_name = self.getPropertyValue("OutputWorkspace") # returns workspace name (string)
+ nhist = self.vanaws.getNumberHistograms()
+ prog_reporter = Progress(self, start=0.0, end=1.0, nreports=nhist+1)
+
+ # calculate array of Debye-Waller factors
+ dwf = self.calculate_dwf()
+
+ # for each detector: fit gaussian to get peak_centre and fwhm
+ # sum data in the range [peak_centre - 3*fwhm, peak_centre + 3*fwhm]
+ dataX = self.vanaws.readX(0)
+ coefY = np.zeros(nhist)
+ coefE = np.zeros(nhist)
+ instrument = self.vanaws.getInstrument()
+ detID_offset = self.get_detID_offset()
+ for idx in range(nhist):
+ prog_reporter.report("Setting %dth spectrum" % idx)
+ dataY = self.vanaws.readY(idx)
+ det = instrument.getDetector(idx + detID_offset)
+ if np.max(dataY) == 0 or det.isMasked():
+ coefY[idx] = 0.
+ coefE[idx] = 0.
+ else:
+ dataE = self.vanaws.readE(idx)
+ peak_centre, sigma = mlzutils.do_fit_gaussian(self.vanaws, idx, self.log())
+ fwhm = sigma*2.*np.sqrt(2.*np.log(2.))
+ idxmin = (np.fabs(dataX-peak_centre+3.*fwhm)).argmin()
+ idxmax = (np.fabs(dataX-peak_centre-3.*fwhm)).argmin()
+ coefY[idx] = dwf[idx]*sum(dataY[idxmin:idxmax+1])
+ coefE[idx] = dwf[idx]*sum(dataE[idxmin:idxmax+1])
+
+ # create X array, X data are the same for all detectors, so
+ coefX = np.zeros(nhist)
+ coefX.fill(dataX[0])
+
+ create = self.createChildAlgorithm("CreateWorkspace")
+ create.setPropertyValue('OutputWorkspace', outws_name)
+ create.setProperty('ParentWorkspace', self.vanaws)
+ create.setProperty('DataX', coefX)
+ create.setProperty('DataY', coefY)
+ create.setProperty('DataE', coefE)
+ create.setProperty('NSpec', nhist)
+ create.setProperty('UnitX', 'TOF')
+ create.execute()
+ outws = create.getProperty('OutputWorkspace').value
+
+ self.setProperty("OutputWorkspace", outws)
+
+ def get_detID_offset(self):
+ """
+ returns ID of the first detector
+ """
+ return self.vanaws.getSpectrum(0).getDetectorIDs()[0]
+
+ def calculate_dwf(self):
+ """
+ Calculates Debye-Waller factor according to
+ Sears and Shelley Acta Cryst. A 47, 441 (1991)
+ """
+ run = self.vanaws.getRun()
+ nhist = self.vanaws.getNumberHistograms()
+ thetasort = np.zeros(nhist) # theta in radians, not 2Theta
+
+ instrument = self.vanaws.getInstrument()
+ detID_offset = self.get_detID_offset()
+
+ for i in range(nhist):
+ det = instrument.getDetector(i + detID_offset)
+ thetasort[i] = 0.5*np.sign(np.cos(det.getPhi()))*self.vanaws.detectorTwoTheta(det)
+ # thetasort[i] = 0.5*self.vanaws.detectorSignedTwoTheta(det) # gives opposite sign for detectors 0-24
+
+ temperature = self.get_temperature() # T in K
+ wlength = float(run.getLogData('wavelength').value) # Wavelength, Angstrom
+ mass_vana = 0.001*self.Mvan/sp.constants.N_A # Vanadium mass, kg
+ temp_ratio = temperature/self.DebyeT
+
+ if temp_ratio < 1.e-3:
+ integral = 0.5
+ else:
+ integral = integrate.quad(lambda x: x/sp.tanh(0.5*x/temp_ratio), 0, 1)[0]
+
+ msd = 3.*sp.constants.hbar**2/(2.*mass_vana*sp.constants.k * self.DebyeT)*integral*1.e20
+ return np.exp(-msd*(4.*sp.pi*sp.sin(thetasort)/wlength)**2)
+
+
+# Register algorithm with Mantid.
+AlgorithmFactory.subscribe(ComputeCalibrationCoefVan)
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
index ffe6574e3e1326047cfee48cf811b073889f061c..32bb98f27c6a938069e1ccb3c01af95a91ac9472 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/DetectorFloodWeighting.py
@@ -86,14 +86,14 @@ class DetectorFloodWeighting(DataProcessorAlgorithm):
divide.setProperty("RHSWorkspace", rhs)
divide.execute()
return divide.getProperty("OutputWorkspace").value
-
+
def _add(self, lhs, rhs):
divide = self.createChildAlgorithm("Plus")
divide.setProperty("LHSWorkspace", lhs)
divide.setProperty("RHSWorkspace", rhs)
divide.execute()
return divide.getProperty("OutputWorkspace").value
-
+
def _integrate_bands(self, bands, in_ws):
# Formulate bands, integrate and sum
accumulated_output = None
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py
index 7fc7669b87706f09e5faec5f0b8e607dcb950867..69a0a5485cf1d5ce2e9d537260f2e60f09e913d5 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/EVSDiffractionReduction.py
@@ -1,3 +1,4 @@
+#pylint: disable=no-init
from mantid.simpleapi import *
from mantid.api import *
from mantid.kernel import *
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
index 960820fb8a070abd43f2ce9f20876c8f4d51428d..461f44dfac4040837f72c838ae4e1d8c4fd1a4a2 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ResNorm2.py
@@ -55,8 +55,8 @@ class ResNorm(PythonAlgorithm):
direction=Direction.Output),
doc='Fitted parameter output')
- self.declareProperty(ITableWorkspaceProperty('OutputWorkspaceTable', '',
- optional=PropertyMode.Optional,
+ self.declareProperty(ITableWorkspaceProperty('OutputWorkspaceTable', '',
+ optional=PropertyMode.Optional,
direction=Direction.Output),
doc='Table workspace of fit parameters')
diff --git a/Framework/PythonInterface/plugins/algorithms/mlzutils.py b/Framework/PythonInterface/plugins/algorithms/mlzutils.py
index 3b69302522b7ef2cd6d2eba41c946e3e548d5673..d0e47dbdc7891c084a714360e66ae6daf3b60f81 100644
--- a/Framework/PythonInterface/plugins/algorithms/mlzutils.py
+++ b/Framework/PythonInterface/plugins/algorithms/mlzutils.py
@@ -1,4 +1,6 @@
import mantid.simpleapi as api
+from mantid.api import AlgorithmManager
+import numpy as np
def cleanup(wslist):
@@ -154,3 +156,69 @@ def compare_mandatory(wslist, plist, logger, tolerance=0.01):
"Workspaces: " + ", ".join(wslist) + "\n Values: " + str(properties)
logger.error(message)
raise RuntimeError(message)
+
+
+def do_fit_gaussian(workspace, index, logger):
+ """
+ Calculates guess values on peak centre, sigma and peak height.
+ Uses them as an input to run a fit algorithm
+ @ param workspace --- input workspace
+ @ param index --- the spectrum with which WorkspaceIndex to fit
+ @ returns peak_centre --- fitted peak centre
+ @ returns sigma --- fitted sigma
+ """
+ nhist = workspace.getNumberHistograms()
+ if index > nhist:
+ message = "Index " + str(index) + " is out of range for the workspace " + workspace.getName()
+ logger.error(message)
+ raise RuntimeError(message)
+
+ x_values = np.array(workspace.readX(index))
+ y_values = np.array(workspace.readY(index))
+
+ # get peak centre position
+ imax = np.argmax(y_values)
+ height = y_values[imax]
+
+ # check for zero or negative signal
+ if height <= 0:
+ logger.warning("Workspace %s, detector %d has maximum <= 0" % (workspace.getName(), index))
+ return [0, 0]
+
+ try_centre = x_values[imax]
+
+ # guess sigma
+ indices = np.argwhere(y_values > 0.5*height)
+ nentries = len(indices)
+ if nentries < 3:
+ message = "Spectrum " + str(index) + " in workspace " + workspace.getName() +\
+ " has too narrow peak. Cannot guess sigma. Check your data."
+ logger.error(message)
+ raise RuntimeError(message)
+ # fwhm = sigma * (2.*np.sqrt(2.*np.log(2.)))
+ fwhm = np.fabs(x_values[indices[nentries - 1, 0]] - x_values[indices[0, 0]])
+ sigma = fwhm/(2.*np.sqrt(2.*np.log(2.)))
+
+ # create and execute Fit algorithm
+ myfunc = 'name=Gaussian, Height='+str(height)+', PeakCentre='+str(try_centre)+', Sigma='+str(sigma)
+ startX = try_centre - 3.0*fwhm
+ endX = try_centre + 3.0*fwhm
+ prefix = "Fit" + workspace.getName() + str(index)
+ fit_alg = AlgorithmManager.createUnmanaged('Fit')
+ fit_alg.initialize()
+ fit_alg.setChild(True)
+ api.set_properties(fit_alg, Function=myfunc, InputWorkspace=workspace, CreateOutput=True, Output=prefix)
+ fit_alg.setProperty('StartX', startX)
+ fit_alg.setProperty('EndX', endX)
+ fit_alg.setProperty('WorkspaceIndex', index)
+ fit_successful = fit_alg.execute()
+ param_table = fit_alg.getProperty('OutputParameters').value
+
+ if not fit_successful:
+ message = "For detector " + str(index) + " in workspace " + workspace.getName() +\
+ "fit was not successful. Input guess parameters are " + str(myfunc)
+ logger.error(message)
+ raise RuntimeError(message)
+
+ # return list: [peak_centre, sigma]
+ return param_table.column(1)[1:3]
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index 06aefc104046e72c2151ed57d7933b8230e6daec..952bb617bfa603aaaedee0c7393bf6f8a7ad9af5 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -8,6 +8,7 @@ set ( TEST_PY_FILES
CalculateSampleTransmissionTest.py
CheckForSampleLogsTest.py
ConjoinSpectraTest.py
+ ComputeCalibrationCoefVanTest.py
CorrectLogTimesTest.py
CreateLeBailFitInputTest.py
CreateMDTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..aff74c2e324ac2e288cce0a16a55727b9000f691
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/ComputeCalibrationCoefVanTest.py
@@ -0,0 +1,82 @@
+import unittest
+from mantid.simpleapi import DeleteWorkspace, CreateSampleWorkspace, AddSampleLog, EditInstrumentGeometry,\
+ CloneWorkspace, CheckWorkspacesMatch
+from testhelpers import run_algorithm
+from mantid.api import AnalysisDataService
+from scipy.constants import N_A, hbar, k
+import numpy as np
+
+
+class ComputeCalibrationCoefVanTest(unittest.TestCase):
+ def setUp(self):
+ input_ws = CreateSampleWorkspace(Function="User Defined",
+ UserDefinedFunction="name=LinearBackground, A0=0.3;name=Gaussian, \
+ PeakCentre=5, Height=10, Sigma=0.3", NumBanks=2, BankPixelWidth=1,
+ XMin=0, XMax=10, BinWidth=0.1, BankDistanceFromSample=4.0)
+ self._input_ws = input_ws
+ AddSampleLog(self._input_ws, LogName='wavelength', LogText='4.0', LogType='Number', LogUnit='Angstrom')
+
+ def test_output(self):
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # Output = Vanadium ws
+ self.assertEqual(wsoutput.getRun().getLogData('run_title').value,
+ self._input_ws.getRun().getLogData('run_title').value)
+
+ # Size of output workspace
+ self.assertEqual(wsoutput.getNumberHistograms(), self._input_ws.getNumberHistograms())
+
+ DeleteWorkspace(wsoutput)
+ return
+
+ def test_sum(self):
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # check whether sum is calculated correctly, for theta=0, dwf=1
+ y_sum = sum(self._input_ws.readY(0)[27:75])
+ self.assertAlmostEqual(y_sum, wsoutput.readY(0)[0])
+
+ DeleteWorkspace(wsoutput)
+
+ def test_dwf(self):
+ outputWorkspaceName = "output_ws"
+
+ # change theta to make dwf != 1
+ EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15", Azimuthal="0,0", DetectorIDs="1,2")
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
+
+ # check dwf calculation
+ y_sum = sum(self._input_ws.readY(1)[27:75])
+ mvan = 0.001*50.942/N_A
+ Bcoef = 4.736767162094296*1e+20*hbar*hbar/(2.0*mvan*k*389.0)
+ dwf = np.exp(-1.0*Bcoef*(4.0*np.pi*np.sin(0.5*np.radians(15.0))/4.0)**2)
+ self.assertAlmostEqual(y_sum*dwf, wsoutput.readY(1)[0])
+
+ DeleteWorkspace(wsoutput)
+
+ def test_input_not_modified(self):
+ backup = CloneWorkspace(self._input_ws)
+ outputWorkspaceName = "output_ws"
+ alg_test = run_algorithm("ComputeCalibrationCoefVan", VanadiumWorkspace=self._input_ws,
+ OutputWorkspace=outputWorkspaceName)
+ self.assertTrue(alg_test.isExecuted())
+ self.assertEqual("Success!", CheckWorkspacesMatch(backup, self._input_ws))
+ DeleteWorkspace(backup)
+
+ def tearDown(self):
+ if AnalysisDataService.doesExist(self._input_ws.getName()):
+ DeleteWorkspace(self._input_ws)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/Framework/WorkflowAlgorithms/inc/MantidWorkflowAlgorithms/MuonCalculateAsymmetry.h b/Framework/WorkflowAlgorithms/inc/MantidWorkflowAlgorithms/MuonCalculateAsymmetry.h
index 70f448d5433155eb5d1fd7ca0cb2d466a832e7bb..0d8c35783d1c54ea3aad93fc4231da183b59000b 100644
--- a/Framework/WorkflowAlgorithms/inc/MantidWorkflowAlgorithms/MuonCalculateAsymmetry.h
+++ b/Framework/WorkflowAlgorithms/inc/MantidWorkflowAlgorithms/MuonCalculateAsymmetry.h
@@ -49,12 +49,22 @@ private:
void init();
void exec();
- /// Converts given workspace according to the OutputType
- API::MatrixWorkspace_sptr convertWorkspace(API::MatrixWorkspace_sptr ws);
-
- /// Merges two period workspaces according to PeriodOperation specified
- API::MatrixWorkspace_sptr mergePeriods(API::MatrixWorkspace_sptr ws1,
- API::MatrixWorkspace_sptr ws2);
+ // Calculates raw counts
+ API::MatrixWorkspace_sptr
+ calculateGroupCounts(const API::MatrixWorkspace_sptr &firstPeriodWS,
+ const API::MatrixWorkspace_sptr &secondPeriodWS,
+ int groupIndex, std::string op);
+ // Calculates asymmetry for specified spectrum
+ API::MatrixWorkspace_sptr
+ calculateGroupAsymmetry(const API::MatrixWorkspace_sptr &firstPeriodWS,
+ const API::MatrixWorkspace_sptr &secondPeriodWS,
+ int groupIndex, std::string op);
+ // Calculates asymmetry for a pair of spectra
+ API::MatrixWorkspace_sptr
+ calculatePairAsymmetry(const API::MatrixWorkspace_sptr &firstPeriodWS,
+ const API::MatrixWorkspace_sptr &secondPeriodWS,
+ int firstPairIndex, int secondPairIndex, double alpha,
+ std::string op);
};
} // namespace WorkflowAlgorithms
diff --git a/Framework/WorkflowAlgorithms/src/MuonCalculateAsymmetry.cpp b/Framework/WorkflowAlgorithms/src/MuonCalculateAsymmetry.cpp
index ee9504bc04cea99fe906da51ab70484da81c0b83..0b5ee591080593aa78fc74fd76f7b8b71f7ed1d1 100644
--- a/Framework/WorkflowAlgorithms/src/MuonCalculateAsymmetry.cpp
+++ b/Framework/WorkflowAlgorithms/src/MuonCalculateAsymmetry.cpp
@@ -107,125 +107,286 @@ void MuonCalculateAsymmetry::exec() {
MatrixWorkspace_sptr firstPeriodWS = getProperty("FirstPeriodWorkspace");
MatrixWorkspace_sptr secondPeriodWS = getProperty("SecondPeriodWorkspace");
- MatrixWorkspace_sptr convertedWS;
+ // The type of calculation
+ const std::string type = getPropertyValue("OutputType");
- if (secondPeriodWS) {
- // Two periods
- MatrixWorkspace_sptr mergedWS = mergePeriods(firstPeriodWS, secondPeriodWS);
- convertedWS = convertWorkspace(mergedWS);
+ // The group index
+ int groupIndex = getProperty("GroupIndex");
+
+ // The type of period operation (+ or -)
+ std::string op = getProperty("PeriodOperation");
+
+ if (type == "GroupCounts") {
+
+ auto outWS =
+ calculateGroupCounts(firstPeriodWS, secondPeriodWS, groupIndex, op);
+
+ setProperty("OutputWorkspace", outWS);
+
+ } else if (type == "GroupAsymmetry") {
+
+ auto outWS =
+ calculateGroupAsymmetry(firstPeriodWS, secondPeriodWS, groupIndex, op);
+
+ setProperty("OutputWorkspace", outWS);
+
+ } else if (type == "PairAsymmetry") {
+
+ int pairFirstIndex = getProperty("PairFirstIndex");
+ int pairSecondIndex = getProperty("PairSecondIndex");
+ double alpha = getProperty("Alpha");
+
+ auto outWS =
+ calculatePairAsymmetry(firstPeriodWS, secondPeriodWS, pairFirstIndex,
+ pairSecondIndex, alpha, op);
+
+ setProperty("OutputWorkspace", outWS);
} else {
- // Single period only
- convertedWS = convertWorkspace(firstPeriodWS);
- }
- setProperty("OutputWorkspace", convertedWS);
+ throw std::invalid_argument("Specified OutputType is not supported");
+ }
}
/**
- * Converts given workspace according to the OutputType.
- * @param ws :: Workspace to convert
- * @return Converted workspace
- */
-MatrixWorkspace_sptr
-MuonCalculateAsymmetry::convertWorkspace(MatrixWorkspace_sptr ws) {
- const std::string type = getPropertyValue("OutputType");
+* Calculates raw counts according to period operation
+* @param firstPeriodWS :: [input] First period workspace
+* @param secondPeriodWS :: [input] Second period workspace
+* @param groupIndex :: [input] Index of the workspace to extract counts from
+* @param op :: [input] Period operation (+ or -)
+*/
+MatrixWorkspace_sptr MuonCalculateAsymmetry::calculateGroupCounts(
+ const MatrixWorkspace_sptr &firstPeriodWS,
+ const MatrixWorkspace_sptr &secondPeriodWS, int groupIndex,
+ std::string op) {
- if (type == "GroupCounts" || type == "GroupAsymmetry") {
- int groupIndex = getProperty("GroupIndex");
+ if (secondPeriodWS) {
+ // Two periods supplied
- if (groupIndex == EMPTY_INT())
- throw std::runtime_error("GroupIndex is not specified");
+ MatrixWorkspace_sptr tempWS;
- // Yank out the counts of requested group
- IAlgorithm_sptr alg = createChildAlgorithm("ExtractSingleSpectrum");
- alg->initialize();
- alg->setProperty("InputWorkspace", ws);
- alg->setProperty("WorkspaceIndex", groupIndex);
- alg->execute();
+ if (op == "+") {
- MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
+ IAlgorithm_sptr alg = createChildAlgorithm("Plus");
+ alg->initialize();
+ alg->setProperty("LHSWorkspace", firstPeriodWS);
+ alg->setProperty("RHSWorkspace", secondPeriodWS);
+ alg->execute();
+ tempWS = alg->getProperty("OutputWorkspace");
- if (type == "GroupAsymmetry") {
- // GroupAsymmetry - counts with ExpDecay removed and normalized
+ } else if (op == "-") {
- IAlgorithm_sptr alg = createChildAlgorithm("RemoveExpDecay");
+ IAlgorithm_sptr alg = createChildAlgorithm("Minus");
alg->initialize();
- alg->setProperty("InputWorkspace", outWS);
+ alg->setProperty("LHSWorkspace", firstPeriodWS);
+ alg->setProperty("RHSWorkspace", secondPeriodWS);
alg->execute();
-
- outWS = alg->getProperty("OutputWorkspace");
+ tempWS = alg->getProperty("OutputWorkspace");
}
- return outWS;
- } else if (type == "PairAsymmetry") {
- // PairAsymmetry - result of AsymmetryCalc algorithm
-
- int pairFirstIndex = getProperty("PairFirstIndex");
- int pairSecondIndex = getProperty("PairSecondIndex");
-
- if (pairFirstIndex == EMPTY_INT() || pairSecondIndex == EMPTY_INT())
- throw std::invalid_argument("Both pair indices should be specified");
-
- double alpha = getProperty("Alpha");
+ IAlgorithm_sptr alg = createChildAlgorithm("ExtractSingleSpectrum");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", tempWS);
+ alg->setProperty("WorkspaceIndex", groupIndex);
+ alg->execute();
+ MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
- // We get pair groups as their workspace indices, but AsymmetryCalc wants
- // spectra numbers,
- // so need to convert
- specid_t spectraNo1 = ws->getSpectrum(pairFirstIndex)->getSpectrumNo();
- specid_t spectraNo2 = ws->getSpectrum(pairSecondIndex)->getSpectrumNo();
+ return outWS;
- if (spectraNo1 == -1 || spectraNo2 == -1 || spectraNo1 == spectraNo2)
- throw std::invalid_argument(
- "Spectra numbers of the input workspace are not set properly");
+ } else {
+ // Only one period supplied
- IAlgorithm_sptr alg = createChildAlgorithm("AsymmetryCalc");
- alg->setProperty("InputWorkspace", ws);
- // As strings, cause otherwise would need to create arrays with single
- // elements
- alg->setPropertyValue("ForwardSpectra",
- boost::lexical_cast<std::string>(spectraNo1));
- alg->setPropertyValue("BackwardSpectra",
- boost::lexical_cast<std::string>(spectraNo2));
- alg->setProperty("Alpha", alpha);
+ IAlgorithm_sptr alg = createChildAlgorithm("ExtractSingleSpectrum");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", firstPeriodWS);
+ alg->setProperty("WorkspaceIndex", groupIndex);
alg->execute();
-
MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
return outWS;
}
-
- throw std::invalid_argument("Specified OutputType is not supported");
}
/**
- * Merges two period workspaces according to PeriodOperation specified.
- * @param ws1 :: First period workspace
- * @param ws2 :: Second period workspace
- * @return Merged workspace
- */
-MatrixWorkspace_sptr
-MuonCalculateAsymmetry::mergePeriods(MatrixWorkspace_sptr ws1,
- MatrixWorkspace_sptr ws2) {
- std::string op = getProperty("PeriodOperation");
+* Calculates single-spectrum asymmetry according to period operation
+* @param firstPeriodWS :: [input] First period workspace
+* @param secondPeriodWS :: [input] Second period workspace
+* @param groupIndex :: [input] Workspace index for which to calculate asymmetry
+* @param op :: [input] Period operation (+ or -)
+*/
+MatrixWorkspace_sptr MuonCalculateAsymmetry::calculateGroupAsymmetry(
+ const MatrixWorkspace_sptr &firstPeriodWS,
+ const MatrixWorkspace_sptr &secondPeriodWS, int groupIndex,
+ std::string op) {
+
+ // The output workspace
+ MatrixWorkspace_sptr tempWS;
+
+ if (secondPeriodWS) {
+ // Two period workspaces where supplied
+
+ if (op == "+") {
- std::string algorithmName;
+ // Sum
+ IAlgorithm_sptr alg = createChildAlgorithm("Plus");
+ alg->initialize();
+ alg->setProperty("LHSWorkspace", firstPeriodWS);
+ alg->setProperty("RHSWorkspace", secondPeriodWS);
+ alg->execute();
+ MatrixWorkspace_sptr sumWS = alg->getProperty("OutputWorkspace");
+
+ // GroupIndex as vector
+ // Necessary if we want RemoveExpDecay to fit only the requested
+ // spectrum
+ std::vector<int> spec(1, groupIndex);
+
+ // Remove decay
+ IAlgorithm_sptr asym = createChildAlgorithm("RemoveExpDecay");
+ asym->setProperty("InputWorkspace", sumWS);
+ asym->setProperty("Spectra", spec);
+ asym->execute();
+ tempWS = asym->getProperty("OutputWorkspace");
+
+ } else if (op == "-") {
+
+ // GroupIndex as vector
+ std::vector<int> spec(1, groupIndex);
+
+ // Remove decay (first period ws)
+ IAlgorithm_sptr asym = createChildAlgorithm("RemoveExpDecay");
+ asym->initialize();
+ asym->setProperty("InputWorkspace", firstPeriodWS);
+ asym->setProperty("Spectra", spec);
+ asym->execute();
+ MatrixWorkspace_sptr asymFirstPeriod =
+ asym->getProperty("OutputWorkspace");
+
+ // Remove decay (second period ws)
+ asym = createChildAlgorithm("RemoveExpDecay");
+ asym->initialize();
+ asym->setProperty("InputWorkspace", secondPeriodWS);
+ asym->setProperty("Spectra", spec);
+ asym->execute();
+ MatrixWorkspace_sptr asymSecondPeriod =
+ asym->getProperty("OutputWorkspace");
+
+ // Now subtract
+ IAlgorithm_sptr alg = createChildAlgorithm("Minus");
+ alg->initialize();
+ alg->setProperty("LHSWorkspace", asymFirstPeriod);
+ alg->setProperty("RHSWorkspace", asymSecondPeriod);
+ alg->execute();
+ tempWS = alg->getProperty("OutputWorkspace");
+ }
+ } else {
+ // Only one period was supplied
- if (op == "+") {
- algorithmName = "Plus";
- } else if (op == "-") {
- algorithmName = "Minus";
+ IAlgorithm_sptr alg = createChildAlgorithm("RemoveExpDecay");
+ alg->initialize();
+ alg->setProperty("InputWorkspace", firstPeriodWS);
+ alg->execute();
+ tempWS = alg->getProperty("OutputWorkspace");
}
- IAlgorithm_sptr alg = createChildAlgorithm(algorithmName);
+ // Extract the requested spectrum
+ IAlgorithm_sptr alg = createChildAlgorithm("ExtractSingleSpectrum");
alg->initialize();
- alg->setProperty("LHSWorkspace", ws1);
- alg->setProperty("RHSWorkspace", ws2);
+ alg->setProperty("InputWorkspace", tempWS);
+ alg->setProperty("WorkspaceIndex", groupIndex);
alg->execute();
-
MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
-
return outWS;
}
+
+/**
+* Calculates pair asymmetry according to period operation
+* @param firstPeriodWS :: [input] First period workspace
+* @param secondPeriodWS :: [input] Second period workspace
+* @param firstPairIndex :: [input] Workspace index for the forward group
+* @param secondPairIndex :: [input] Workspace index for the backward group
+* @param alpha :: [input] The balance parameter
+* @param op :: [input] Period operation (+ or -)
+*/
+MatrixWorkspace_sptr MuonCalculateAsymmetry::calculatePairAsymmetry(
+ const MatrixWorkspace_sptr &firstPeriodWS,
+ const MatrixWorkspace_sptr &secondPeriodWS, int firstPairIndex,
+ int secondPairIndex, double alpha, std::string op) {
+
+ // Pair indices as vectors
+ std::vector<int> fwd(1, firstPairIndex + 1);
+ std::vector<int> bwd(1, secondPairIndex + 1);
+
+ if (secondPeriodWS) {
+
+ MatrixWorkspace_sptr outWS;
+
+ if (op == "+") {
+
+ // Sum
+ IAlgorithm_sptr alg = createChildAlgorithm("Plus");
+ alg->initialize();
+ alg->setProperty("LHSWorkspace", firstPeriodWS);
+ alg->setProperty("RHSWorkspace", secondPeriodWS);
+ alg->execute();
+ MatrixWorkspace_sptr sumWS = alg->getProperty("OutputWorkspace");
+
+ // Asymmetry calculation
+ alg = createChildAlgorithm("AsymmetryCalc");
+ alg->setProperty("InputWorkspace", sumWS);
+ alg->setProperty("ForwardSpectra", fwd);
+ alg->setProperty("BackwardSpectra", bwd);
+ alg->setProperty("Alpha", alpha);
+ alg->execute();
+ outWS = alg->getProperty("OutputWorkspace");
+
+ } else if (op == "-") {
+
+ std::vector<int> fwd(1, firstPairIndex + 1);
+ std::vector<int> bwd(1, secondPairIndex + 1);
+
+ // First period asymmetry
+ IAlgorithm_sptr alg = createChildAlgorithm("AsymmetryCalc");
+ alg->setProperty("InputWorkspace", firstPeriodWS);
+ alg->setProperty("ForwardSpectra", fwd);
+ alg->setProperty("BackwardSpectra", bwd);
+ alg->setProperty("Alpha", alpha);
+ alg->execute();
+ MatrixWorkspace_sptr asymFirstPeriod =
+ alg->getProperty("OutputWorkspace");
+
+ // Second period asymmetry
+ alg = createChildAlgorithm("AsymmetryCalc");
+ alg->setProperty("InputWorkspace", secondPeriodWS);
+ alg->setProperty("ForwardSpectra", fwd);
+ alg->setProperty("BackwardSpectra", bwd);
+ alg->setProperty("Alpha", alpha);
+ alg->execute();
+ MatrixWorkspace_sptr asymSecondPeriod =
+ alg->getProperty("OutputWorkspace");
+
+ // Now subtract
+ alg = createChildAlgorithm("Minus");
+ alg->initialize();
+ alg->setProperty("LHSWorkspace", asymFirstPeriod);
+ alg->setProperty("RHSWorkspace", asymSecondPeriod);
+ alg->execute();
+ outWS = alg->getProperty("OutputWorkspace");
+ }
+
+ return outWS;
+
+ } else {
+
+ IAlgorithm_sptr alg = createChildAlgorithm("AsymmetryCalc");
+ alg->setProperty("InputWorkspace", firstPeriodWS);
+ alg->setProperty("ForwardSpectra", fwd);
+ alg->setProperty("BackwardSpectra", bwd);
+ alg->setProperty("Alpha", alpha);
+ alg->execute();
+ MatrixWorkspace_sptr outWS = alg->getProperty("OutputWorkspace");
+
+ return outWS;
+ }
+}
} // namespace WorkflowAlgorithms
} // namespace Mantid
diff --git a/Framework/WorkflowAlgorithms/src/RefReduction.cpp b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
index 9cc5678a2d2df87113a607c4a9ac52bc0976f26b..5a85b6b69186405fdeae7e31bee928b7e11f1dd3 100644
--- a/Framework/WorkflowAlgorithms/src/RefReduction.cpp
+++ b/Framework/WorkflowAlgorithms/src/RefReduction.cpp
@@ -612,16 +612,35 @@ double RefReduction::calculateAngleREFM(MatrixWorkspace_sptr workspace) {
double dangle = getProperty("DetectorAngle");
if (isEmpty(dangle)) {
Mantid::Kernel::Property *prop = workspace->run().getProperty("DANGLE");
+ if (!prop) {
+ throw std::runtime_error("DetectorAngle property not given as input, and "
+ "could not find the log entry DANGLE either");
+ }
Mantid::Kernel::TimeSeriesProperty<double> *dp =
dynamic_cast<Mantid::Kernel::TimeSeriesProperty<double> *>(prop);
+ if (!dp) {
+ throw std::runtime_error(
+ "The log entry DANGLE could not"
+ "be interpreted as a property of type time series of double");
+ }
dangle = dp->getStatistics().mean;
}
double dangle0 = getProperty("DetectorAngle0");
if (isEmpty(dangle0)) {
Mantid::Kernel::Property *prop = workspace->run().getProperty("DANGLE0");
+ if (!prop) {
+ throw std::runtime_error("DetectorAngle0 property not given aas input, "
+ "and could not find the log entry DANGLE0 "
+ "either");
+ }
Mantid::Kernel::TimeSeriesProperty<double> *dp =
dynamic_cast<Mantid::Kernel::TimeSeriesProperty<double> *>(prop);
+ if (!dp) {
+ throw std::runtime_error(
+ "The log entry DANGLE0 could not "
+ "be interpreted as a property of type time series of double values");
+ }
dangle0 = dp->getStatistics().mean;
}
diff --git a/Framework/WorkflowAlgorithms/test/MuonCalculateAsymmetryTest.h b/Framework/WorkflowAlgorithms/test/MuonCalculateAsymmetryTest.h
index 0d2038ad16f5aca37a804114647c0c3dfd1a2e9e..8b19f4693fb2f5ab6e98d44afdd88dafa5c84f35 100644
--- a/Framework/WorkflowAlgorithms/test/MuonCalculateAsymmetryTest.h
+++ b/Framework/WorkflowAlgorithms/test/MuonCalculateAsymmetryTest.h
@@ -171,7 +171,7 @@ public:
AnalysisDataService::Instance().remove(outWSName);
}
- void test_groupAsymmetry() {
+ void test_groupAsymmetry_singlePeriod() {
// Name of the output workspace.
const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
@@ -213,7 +213,96 @@ public:
AnalysisDataService::Instance().remove(outWSName);
}
- void test_pairAsymmetry() {
+ void test_groupAsymmetry_twoPeriods_minus() {
+ // Name of the output workspace.
+ const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
+
+ MatrixWorkspace_sptr inWS = createWorkspace(3);
+ MatrixWorkspace_sptr inWSSecond = createWorkspace();
+
+ MuonCalculateAsymmetry alg;
+ alg.initialize();
+ alg.setProperty("FirstPeriodWorkspace", inWS);
+ alg.setProperty("SecondPeriodWorkspace", inWSSecond);
+ alg.setProperty("PeriodOperation", "-");
+ alg.setProperty("OutputType", "GroupAsymmetry");
+ alg.setProperty("GroupIndex", 2);
+ alg.setPropertyValue("OutputWorkspace", outWSName);
+ TS_ASSERT_THROWS_NOTHING(alg.execute(););
+ TS_ASSERT(alg.isExecuted());
+
+ // Retrieve the workspace from data service.
+ auto ws =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outWSName);
+ TS_ASSERT(ws);
+
+ if (ws) {
+ TS_ASSERT_EQUALS(ws->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(ws->blocksize(), 3);
+
+ TS_ASSERT_EQUALS(ws->readX(0)[0], 1);
+ TS_ASSERT_EQUALS(ws->readX(0)[1], 2);
+ TS_ASSERT_EQUALS(ws->readX(0)[2], 3);
+
+ TS_ASSERT_DELTA(ws->readY(0)[0], 0.0030, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[1], -0.0455, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[2], -0.1511, 0.0001);
+
+ TS_ASSERT_DELTA(ws->readE(0)[0], 0.1066, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[1], 0.1885, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[2], 0.3295, 0.0001);
+ }
+
+ // Remove workspace from the data service.
+ AnalysisDataService::Instance().remove(outWSName);
+ }
+
+ void test_groupAsymmetry_twoPeriods_plus() {
+
+ // Name of the output workspace.
+ const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
+
+ MatrixWorkspace_sptr inWS = createWorkspace(3);
+ MatrixWorkspace_sptr inWSSecond = createWorkspace();
+
+ MuonCalculateAsymmetry alg;
+ alg.initialize();
+ alg.setProperty("FirstPeriodWorkspace", inWS);
+ alg.setProperty("SecondPeriodWorkspace", inWSSecond);
+ alg.setProperty("PeriodOperation", "+");
+ alg.setProperty("OutputType", "GroupAsymmetry");
+ alg.setProperty("GroupIndex", 1);
+ alg.setPropertyValue("OutputWorkspace", outWSName);
+ TS_ASSERT_THROWS_NOTHING(alg.execute(););
+ TS_ASSERT(alg.isExecuted());
+
+ // Retrieve the workspace from data service.
+ auto ws =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outWSName);
+ TS_ASSERT(ws);
+
+ if (ws) {
+ TS_ASSERT_EQUALS(ws->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(ws->blocksize(), 3);
+
+ TS_ASSERT_EQUALS(ws->readX(0)[0], 1);
+ TS_ASSERT_EQUALS(ws->readX(0)[1], 2);
+ TS_ASSERT_EQUALS(ws->readX(0)[2], 3);
+
+ TS_ASSERT_DELTA(ws->readY(0)[0], -0.2529, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[1], 0.3918, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[2], 1.5316, 0.0001);
+
+ TS_ASSERT_DELTA(ws->readE(0)[0], 0.0547, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[1], 0.1010, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[2], 0.1825, 0.0001);
+ }
+
+ // Remove workspace from the data service.
+ AnalysisDataService::Instance().remove(outWSName);
+ }
+
+ void test_pairAsymmetry_singlePeriod() {
// Name of the output workspace.
const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
@@ -257,6 +346,98 @@ public:
AnalysisDataService::Instance().remove(outWSName);
}
+ void test_pairAsymmetry_twoPeriods_minus() {
+ // Name of the output workspace.
+ const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
+
+ MatrixWorkspace_sptr inWS = createWorkspace(3);
+ MatrixWorkspace_sptr inWSSecond = createWorkspace();
+
+ MuonCalculateAsymmetry alg;
+ alg.initialize();
+ alg.setProperty("FirstPeriodWorkspace", inWS);
+ alg.setProperty("SecondPeriodWorkspace", inWSSecond);
+ alg.setProperty("PeriodOperation", "-");
+ alg.setProperty("OutputType", "PairAsymmetry");
+ alg.setProperty("PeriodOperation", "-");
+ alg.setProperty("PairFirstIndex", 2);
+ alg.setProperty("PairSecondIndex", 0);
+ alg.setPropertyValue("OutputWorkspace", outWSName);
+ TS_ASSERT_THROWS_NOTHING(alg.execute());
+ TS_ASSERT(alg.isExecuted());
+
+ // Retrieve the workspace from data service.
+ auto ws =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outWSName);
+ TS_ASSERT(ws);
+
+ if (ws) {
+ TS_ASSERT_EQUALS(ws->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(ws->blocksize(), 3);
+
+ TS_ASSERT_DELTA(ws->readY(0)[0], -0.3214, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[1], -0.2250, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[2], -0.1666, 0.0001);
+
+ TS_ASSERT_EQUALS(ws->readX(0)[0], 1.5);
+ TS_ASSERT_EQUALS(ws->readX(0)[1], 2.5);
+ TS_ASSERT_EQUALS(ws->readX(0)[2], 3);
+
+ TS_ASSERT_DELTA(ws->readE(0)[0], 0.5290, 0.001);
+ TS_ASSERT_DELTA(ws->readE(0)[1], 0.4552, 0.001);
+ TS_ASSERT_DELTA(ws->readE(0)[2], 0.4073, 0.001);
+ }
+
+ // Remove workspace from the data service.
+ AnalysisDataService::Instance().remove(outWSName);
+ }
+
+ void test_pairAsymmetry_twoPeriods_plus() {
+
+ // Name of the output workspace.
+ const std::string outWSName = outputWorkspaceName("GroupAsymmetry");
+
+ MatrixWorkspace_sptr inWS = createWorkspace(3);
+ MatrixWorkspace_sptr inWSSecond = createWorkspace();
+
+ MuonCalculateAsymmetry alg;
+ alg.initialize();
+ alg.setProperty("FirstPeriodWorkspace", inWS);
+ alg.setProperty("SecondPeriodWorkspace", inWSSecond);
+ alg.setProperty("PeriodOperation", "+");
+ alg.setProperty("OutputType", "PairAsymmetry");
+ alg.setProperty("PairFirstIndex", 0);
+ alg.setProperty("PairSecondIndex", 2);
+ alg.setPropertyValue("OutputWorkspace", outWSName);
+ TS_ASSERT_THROWS_NOTHING(alg.execute(););
+ TS_ASSERT(alg.isExecuted());
+
+ // Retrieve the workspace from data service.
+ auto ws =
+ AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outWSName);
+ TS_ASSERT(ws);
+
+ if (ws) {
+ TS_ASSERT_EQUALS(ws->getNumberHistograms(), 1);
+ TS_ASSERT_EQUALS(ws->blocksize(), 3);
+
+ TS_ASSERT_EQUALS(ws->readX(0)[0], 1.5);
+ TS_ASSERT_EQUALS(ws->readX(0)[1], 2.5);
+ TS_ASSERT_EQUALS(ws->readX(0)[2], 3);
+
+ TS_ASSERT_DELTA(ws->readY(0)[0], -0.5454, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[1], -0.4615, 0.0001);
+ TS_ASSERT_DELTA(ws->readY(0)[2], -0.4000, 0.0001);
+
+ TS_ASSERT_DELTA(ws->readE(0)[0], 0.2428, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[1], 0.2159, 0.0001);
+ TS_ASSERT_DELTA(ws->readE(0)[2], 0.1966, 0.0001);
+ }
+
+ // Remove workspace from the data service.
+ AnalysisDataService::Instance().remove(outWSName);
+ }
+
private:
std::string outputWorkspaceName(std::string testName) {
return "MuonCalculateAsymmetryTest_" + testName + "_OutputWS";
diff --git a/MantidPlot/src/Graph.cpp b/MantidPlot/src/Graph.cpp
index b90d59c0c2ba39d003eb0589957f4663b3ab805e..2fbfe1977b7b92b4614dbd36e78c743f457c99d5 100644
--- a/MantidPlot/src/Graph.cpp
+++ b/MantidPlot/src/Graph.cpp
@@ -1290,7 +1290,7 @@ void Graph::linColor()
notifyChanges();
}
-void Graph::setAxisScale(int axis, double start, double end, int type, double step,
+void Graph::setAxisScale(int axis, double start, double end, int scaleType, double step,
int majorTicks, int minorTicks)
{
ScaleEngine *sc_engine = dynamic_cast<ScaleEngine *>(d_plot->axisScaleEngine(axis));
@@ -1300,19 +1300,30 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
ScaleTransformation::Type old_type = sc_engine->type();
// If not specified, keep the same as now
- if( type < 0 ) type = axisType(axis);
+ if( scaleType < 0 ) scaleType = axisType(axis);
- if (type != old_type)
+ int type = ScaleTransformation::Linear;
+ // just to have the one-by-one ScaleType => GraphOptions; higher values of ScaleType
+ // will be GraphOptions::Linear
+ if (ScaleDraw::ScaleType::Numeric == scaleType) {
+ type = ScaleTransformation::Linear;
+ } else if (ScaleDraw::ScaleType::Text == scaleType) {
+ type = ScaleTransformation::Log10;
+ } else if (ScaleDraw::ScaleType::Day == scaleType) {
+ type = ScaleTransformation::Power;
+ }
+
+ if (static_cast<int>(type) != static_cast<int>(old_type))
{
// recalculate boundingRect of MantidCurves
- emit axisScaleChanged(axis,type == ScaleTransformation::Log10);
+ emit axisScaleChanged(axis, type == ScaleTransformation::Log10);
}
- if (type == GraphOptions::Log10)
+ if (type == ScaleTransformation::Log10)
{
sc_engine->setType(ScaleTransformation::Log10);
}
- else if (type == GraphOptions::Power)
+ else if (type == ScaleTransformation::Power)
{
sc_engine->setType(ScaleTransformation::Power);
}
@@ -1321,7 +1332,7 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
sc_engine->setType(ScaleTransformation::Linear);
}
- if (type == GraphOptions::Log10)
+ if (type == ScaleTransformation::Log10)
{
if (start <= 0)
{
@@ -1368,7 +1379,7 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
// log scales can't represent zero or negative values, 1e-10 is a low number that I hope will be lower than most of the data but is still sensible for many color plots
//start = start < 1e-90 ? 1e-10 : start;
}
- else if (type == GraphOptions::Power)
+ else if (type == ScaleTransformation::Power)
{
double const nth_power = sc_engine->nthPower();
if (start <= 0 && nth_power < 0)
@@ -1440,8 +1451,7 @@ void Graph::setAxisScale(int axis, double start, double end, int type, double st
QwtScaleWidget *rightAxis = d_plot->axisWidget(QwtPlot::yRight);
if(rightAxis)
{
- //if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
- if (type == GraphOptions::Log10 && (start <= 0 || start == DBL_MAX))
+ if (type == ScaleTransformation::Log10 && (start <= 0 || start == DBL_MAX))
{
start = sp->getMinPositiveValue();
}
diff --git a/MantidPlot/src/Graph.h b/MantidPlot/src/Graph.h
index 34ae08f03ca7eacf89224cf0b37a0bffcc81b19d..0b3cdbecd8d2eec45c4f3cb4d9bfe6af4b2101f2 100644
--- a/MantidPlot/src/Graph.h
+++ b/MantidPlot/src/Graph.h
@@ -385,7 +385,7 @@ public slots:
void setScale(QwtPlot::Axis axis, QString logOrLin);
double axisStep(int axis){return d_user_step[axis];};
//! Set the axis scale
- void setAxisScale(int axis, double start, double end, int type = -1, double step = 0.0,
+ void setAxisScale(int axis, double start, double end, int scaleType = -1, double step = 0.0,
int majorTicks = 5, int minorTicks = 5);
/// in plot windows change both axis to log-log
diff --git a/MantidPlot/src/ImportASCIIDialog.cpp b/MantidPlot/src/ImportASCIIDialog.cpp
index 075910ef35fb89d929af75626a20ae8a6845b781..f8b10566e93fa4cb43a9ed5ad25385d6a984380c 100644
--- a/MantidPlot/src/ImportASCIIDialog.cpp
+++ b/MantidPlot/src/ImportASCIIDialog.cpp
@@ -464,7 +464,7 @@ void ImportASCIIDialog::previewTable()
int importMode = d_import_mode->currentIndex();
if (importMode == NewTables) {
- importMode = (ImportASCIIDialog::ImportMode)Table::Overwrite;
+ importMode = ImportASCIIDialog::NewWorkspace; //(ImportASCIIDialog::ImportMode)Table::Overwrite;
} else {
importMode -= 2;
}
@@ -494,7 +494,7 @@ void ImportASCIIDialog::previewMatrix() {
int importMode = d_import_mode->currentIndex();
if (importMode == NewMatrices) {
- importMode = (ImportASCIIDialog::ImportMode)Matrix::Overwrite;
+ importMode = ImportASCIIDialog::NewWorkspace; //(ImportASCIIDialog::ImportMode)Matrix::Overwrite;
} else {
// Overwrite-2 => NewColumns (in both Matrix::importMode and
// ImportASCIIDialog::importMode)
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
index ab2f48dfa2db8daac520f43ab82517c3a5325e67..e57514b3b0750f06dbcc794cdfd578ea1efc4e4c 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/QtReflMainView.h
@@ -95,6 +95,7 @@ public:
virtual std::string getSearchString() const;
virtual boost::shared_ptr<IReflPresenter> getPresenter() const;
+
private:
// initialise the interface
virtual void initLayout();
@@ -143,7 +144,7 @@ private slots:
void showSearchContextMenu(const QPoint &pos);
};
-} // namespace CustomInterfaces
} // namespace Mantid
+} // namespace CustomInterfaces
#endif /* MANTID_CUSTOMINTERFACES_QTREFLMAINVIEW_H_ */
diff --git a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
index bfcca663b78dc95a9e99974146d2ec1d066007fb..a60b2df5525e7d4ef0a35effba9220db034e6313 100644
--- a/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
+++ b/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ReflMainView.h
@@ -59,6 +59,10 @@ namespace MantidQt
virtual void showAlgorithmDialog(const std::string& algorithm) = 0;
virtual std::string requestNotebookPath() = 0;
+ //Settings
+ virtual void saveSettings(const std::map<std::string,QVariant>& options) = 0;
+ virtual void loadSettings(std::map<std::string,QVariant>& options) = 0;
+
//Plotting
virtual void plotWorkspaces(const std::set<std::string>& workspaces) = 0;
diff --git a/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp b/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
index 07fef6447c8a24678b514740f03f64a9664d855f..e38a224bff1f2b19cf1dbf3c3bad6b7a724deb5e 100644
--- a/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
+++ b/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
@@ -28,7 +28,8 @@ namespace IDA {
ConvFit::ConvFit(QWidget *parent)
: IndirectDataAnalysisTab(parent), m_stringManager(NULL), m_cfTree(NULL),
- m_fixedProps(), m_cfInputWS(), m_cfInputWSName(), m_confitResFileType() {
+ m_fixedProps(), m_cfInputWS(), m_cfInputWSName(), m_confitResFileType(),
+ m_runMin(-1), m_runMax(-1) {
m_uiForm.setupUi(parent);
}
@@ -996,7 +997,7 @@ void ConvFit::updatePlot() {
return;
if ((specNo - m_runMin) >= 0) {
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(
- outputGroup->getItem(specNo- m_runMin));
+ outputGroup->getItem(specNo - m_runMin));
if (ws) {
m_uiForm.ppPlot->addSpectrum("Fit", ws, 1, Qt::red);
m_uiForm.ppPlot->addSpectrum("Diff", ws, 2, Qt::blue);
@@ -1102,8 +1103,7 @@ void ConvFit::singleFit() {
runPythonCode(
QString(
"from IndirectCommon import getWSprefix\nprint getWSprefix('") +
- m_cfInputWSName + QString("')\n"))
- .trimmed();
+ m_cfInputWSName + QString("')\n")).trimmed();
m_singleFitOutputName +=
QString("conv_") + fitType + bgType + m_uiForm.spPlotSpectrum->text();
int maxIterations =
diff --git a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
index f3632eaf125e82c4d98e20af56f2a998ad70bcea..2723cd05a2779d7712ba4611ec522047e81dda1a 100644
--- a/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
+++ b/MantidQt/CustomInterfaces/src/QtReflMainView.cpp
@@ -8,6 +8,12 @@
#include <qinputdialog.h>
#include <qmessagebox.h>
+
+namespace
+{
+ const QString ReflSettingsGroup = "Mantid/CustomInterfaces/ISISReflectometry";
+}
+
namespace MantidQt
{
namespace CustomInterfaces
@@ -450,6 +456,33 @@ namespace MantidQt
return qfilename.toStdString();
}
+ /**
+ Save settings
+ @param options : map of user options to save
+ */
+ void QtReflMainView::saveSettings(const std::map<std::string,QVariant>& options)
+ {
+ QSettings settings;
+ settings.beginGroup(ReflSettingsGroup);
+ for(auto it = options.begin(); it != options.end(); ++it)
+ settings.setValue(QString::fromStdString(it->first), it->second);
+ settings.endGroup();
+ }
+
+ /**
+ Load settings
+ @param options : map of user options to load into
+ */
+ void QtReflMainView::loadSettings(std::map<std::string,QVariant>& options)
+ {
+ QSettings settings;
+ settings.beginGroup(ReflSettingsGroup);
+ QStringList keys = settings.childKeys();
+ for(auto it = keys.begin(); it != keys.end(); ++it)
+ options[it->toStdString()] = settings.value(*it);
+ settings.endGroup();
+ }
+
/**
Plot a workspace
*/
diff --git a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
index 2aedd280cf80054880642b336291837ffc642aa8..9323fb9b10cc1e91839a520a0f17ac3b65a302f9 100644
--- a/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
+++ b/MantidQt/CustomInterfaces/src/ReflMainViewPresenter.cpp
@@ -24,9 +24,6 @@
#include <fstream>
#include <sstream>
-#include <QSettings>
-#include <QFileDialog>
-
using namespace Mantid::API;
using namespace Mantid::Geometry;
@@ -36,7 +33,6 @@ using namespace MantidQt::MantidWidgets;
namespace
{
- const QString ReflSettingsGroup = "Mantid/CustomInterfaces/ISISReflectometry";
void validateModel(ITableWorkspace_sptr model)
{
@@ -1511,11 +1507,7 @@ namespace MantidQt
m_options[it->first] = it->second;
//Save any changes to disk
- QSettings settings;
- settings.beginGroup(ReflSettingsGroup);
- for(auto it = m_options.begin(); it != m_options.end(); ++it)
- settings.setValue(QString::fromStdString(it->first), it->second);
- settings.endGroup();
+ m_view->saveSettings(m_options);
}
/** Load options from disk if possible, or set to defaults */
@@ -1537,12 +1529,7 @@ namespace MantidQt
m_options["RoundDQQPrecision"] = 3;
//Load saved values from disk
- QSettings settings;
- settings.beginGroup(ReflSettingsGroup);
- QStringList keys = settings.childKeys();
- for(auto it = keys.begin(); it != keys.end(); ++it)
- m_options[it->toStdString()] = settings.value(*it);
- settings.endGroup();
+ m_view->loadSettings(m_options);
}
}
}
diff --git a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
index 026b49d21b3e9966e32a84f26c1b3df3b72ea023..e42a5a70d0bc573e435fb47faf22d0f7b0a6a2b6 100644
--- a/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
+++ b/MantidQt/CustomInterfaces/test/ReflMainViewMockObjects.h
@@ -57,6 +57,8 @@ public:
virtual void setProgress(int) {};
virtual void setTableList(const std::set<std::string>&) {};
virtual void setInstrumentList(const std::vector<std::string>&, const std::string&) {};
+ virtual void saveSettings(const std::map<std::string,QVariant>&) {};
+ virtual void loadSettings(std::map<std::string,QVariant>&) {};
virtual std::string getProcessInstrument() const {return "FAKE";}
virtual boost::shared_ptr<IReflPresenter> getPresenter() const {return boost::shared_ptr<IReflPresenter>();}
};
diff --git a/MantidQt/Python/mantidqt.sip b/MantidQt/Python/mantidqt.sip
index 47824677bf3e1bcd8e3a02a951fbbfa38afd5ad5..8278d788941a600a84f1dd6cc448d1fde138bc8f 100644
--- a/MantidQt/Python/mantidqt.sip
+++ b/MantidQt/Python/mantidqt.sip
@@ -1171,9 +1171,9 @@ void SliceViewer::setRebinNumBins(int xBins, int yBins)
%End
- void setRebinMode(bool mode, bool locked) throw (std::runtime_error);
+ void setRebinMode(bool mode) throw (std::runtime_error);
%Docstring
-void SliceViewer::setRebinMode(bool mode, bool locked)
+void SliceViewer::setRebinMode(bool mode)
------------------------------------------------------
Sets the SliceViewer in dynamic rebin mode.
In this mode, the current view area (see setXYLimits()) is used as the
@@ -1183,8 +1183,6 @@ void SliceViewer::setRebinMode(bool mode, bool locked)
Args:
mode :: true for rebinning mode
- locked :: if true, then the rebinned area is only refreshed manually
- or when changing rebinning parameters.
%End
diff --git a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
index f2eded1e2fa66061992d0583adf13527708f6afc..75014b4c584c09308350b1e6a85956cc64fa9d8a 100644
--- a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
+++ b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.h
@@ -117,7 +117,7 @@ public:
/// Dynamic Rebinning-related Python bindings
void setRebinThickness(int dim, double thickness);
void setRebinNumBins(int xBins, int yBins);
- void setRebinMode(bool mode, bool locked);
+ void setRebinMode(bool mode);
void refreshRebin();
/// Methods relating to peaks overlays.
@@ -188,7 +188,6 @@ public slots:
void LineMode_toggled(bool);
void SnapToGrid_toggled(bool);
void RebinMode_toggled(bool);
- void RebinLock_toggled(bool);
void autoRebin_toggled(bool);
// Dynamic rebinning
@@ -333,7 +332,7 @@ private:
/// Synced menu/buttons
MantidQt::API::SyncedCheckboxes *m_syncLineMode, *m_syncSnapToGrid,
- *m_syncRebinMode, *m_syncRebinLock, *m_syncAutoRebin;
+ *m_syncRebinMode, *m_syncAutoRebin;
/// Cached double for infinity
double m_inf;
diff --git a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
index 9414476bc32f0f92da829ed186475e2fdcb485cb..d3b64c0df10eab853bd8fcc3abe0e5fe74e5c353 100644
--- a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
+++ b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/SliceViewer.ui
@@ -489,47 +489,6 @@
</property>
</widget>
</item>
- <item>
- <widget class="QToolButton" name="btnRebinLock">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>45</width>
- <height>45</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>45</width>
- <height>45</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Lock the rebinned workspace in place (use the refresh button to refresh)</string>
- </property>
- <property name="text">
- <string>...</string>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/SliceViewer/icons/stock-lock.png</normaloff>:/SliceViewer/icons/stock-lock.png</iconset>
- </property>
- <property name="iconSize">
- <size>
- <width>32</width>
- <height>32</height>
- </size>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
<item>
<spacer name="horizontalSpacer_5">
<property name="orientation">
diff --git a/MantidQt/SliceViewer/src/SliceViewer.cpp b/MantidQt/SliceViewer/src/SliceViewer.cpp
index f251baaf4445e9f32142a3d54ea3d16ef6fe62a6..34bba3a13bc370f18250ec802dc46ad8a141908e 100644
--- a/MantidQt/SliceViewer/src/SliceViewer.cpp
+++ b/MantidQt/SliceViewer/src/SliceViewer.cpp
@@ -122,8 +122,6 @@ SliceViewer::SliceViewer(QWidget *parent)
// hide unused buttons
ui.btnZoom->hide(); // hidden for a long time
- ui.btnRebinLock->hide(); // now replaced by auto rebin mode
- // ui.btnClearLine->hide(); // turning off line mode now removes line
// ----------- Toolbar button signals ----------------
QObject::connect(ui.btnResetZoom, SIGNAL(clicked()), this, SLOT(resetZoom()));
@@ -379,13 +377,6 @@ void SliceViewer::initMenus() {
SLOT(RebinMode_toggled(bool)));
m_menuView->addAction(action);
- action = new QAction(QPixmap(), "&Lock Rebinned WS", this);
- m_syncRebinLock = new SyncedCheckboxes(action, ui.btnRebinLock, true);
- connect(m_syncRebinLock, SIGNAL(toggled(bool)), this,
- SLOT(RebinLock_toggled(bool)));
- action->setVisible(false); // hide this action
- m_menuView->addAction(action);
-
action = new QAction(QPixmap(), "Rebin Current View", this);
action->setShortcut(Qt::Key_R + Qt::ControlModifier);
action->setEnabled(false);
@@ -691,7 +682,6 @@ void SliceViewer::setWorkspace(Mantid::API::IMDWorkspace_sptr ws) {
// Can't use dynamic rebin mode with a MatrixWorkspace
m_syncRebinMode->setEnabled(!matrix);
- m_syncRebinLock->setEnabled(!matrix);
// Go to no normalization by default for MatrixWorkspaces
if (matrix)
@@ -1008,13 +998,10 @@ void SliceViewer::setRebinNumBins(int xBins, int yBins) {
* See setRebinThickness() to adjust the thickness in other dimensions.
*
* @param mode :: true for rebinning mode
- * @param locked :: if true, then the rebinned area is only refreshed manually
- * or when changing rebinning parameters.
*/
-void SliceViewer::setRebinMode(bool mode, bool locked) {
+void SliceViewer::setRebinMode(bool mode) {
// The events associated with these controls will trigger a re-draw
m_syncRebinMode->toggle(mode);
- m_syncRebinLock->toggle(locked);
}
//------------------------------------------------------------------------------
@@ -1098,7 +1085,6 @@ void SliceViewer::RebinMode_toggled(bool checked) {
for (size_t d = 0; d < m_dimWidgets.size(); d++)
m_dimWidgets[d]->showRebinControls(checked);
ui.btnRebinRefresh->setEnabled(checked);
- ui.btnRebinLock->setEnabled(checked);
m_syncAutoRebin->setEnabled(checked);
m_actionRefreshRebin->setEnabled(checked);
m_rebinMode = checked;
@@ -1118,17 +1104,6 @@ void SliceViewer::RebinMode_toggled(bool checked) {
}
}
-//------------------------------------------------------------------------------
-/** Slot called when locking/unlocking the dynamically rebinned
- * overlaid workspace
- * @param checked :: DO lock the workspace in place
- */
-void SliceViewer::RebinLock_toggled(bool checked) {
- m_rebinLocked = checked;
- // Rebin immediately
- if (!m_rebinLocked && m_rebinMode)
- this->rebinParamsChanged();
-}
//------------------------------------------------------------------------------
/// Slot for zooming into
diff --git a/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py b/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
index f7ac61b15e55516acb33bf420257de185ef081dc..cff5c28c1d8bc20a66cc35ae89fff4f6f0cb077d 100644
--- a/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
+++ b/MantidQt/SliceViewer/test/SliceViewerPythonInterfaceTest.py
@@ -449,7 +449,7 @@ class SliceViewerPythonInterfaceTest(unittest.TestCase):
sv.setRebinThickness(2, 1.0)
sv.setRebinNumBins(50, 200)
sv.refreshRebin()
- sv.setRebinMode(True, True)
+ sv.setRebinMode(True)
time.sleep(1)
self.assertTrue(mtd.doesExist('uniform_rebinned'), 'Dynamically rebinned workspace was created.')
ws = mtd['uniform_rebinned']
diff --git a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
index 70f51e4427d150b0679b9fa6579287cf043b1e07..299d6d5dc17f3a001ae3e1cb7aa485ce5db73da2 100644
--- a/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
+++ b/Testing/SystemTests/tests/analysis/ValidateInstrumentDefinitionFiles.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#pylint: disable=no-init
from mantid import config
import os
diff --git a/Testing/SystemTests/tests/analysis/reference/MuonLoad_MUSR00015192.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/MuonLoad_MUSR00015192.nxs.md5
index 26060d7d5d3cf334ac8181df8c1433b7d1113530..f5e0395c9f732ac49915ea272c372dda1a7c5366 100644
--- a/Testing/SystemTests/tests/analysis/reference/MuonLoad_MUSR00015192.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/MuonLoad_MUSR00015192.nxs.md5
@@ -1 +1 @@
-f9f8aee9e15f495f43a9846da7adad3e
+75b425bdf72f1d82bb78e0c71a7fe2ca
diff --git a/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst b/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..47661c2ffe102b08e1a498d0c60dc5ee66232113
--- /dev/null
+++ b/docs/source/algorithms/ComputeCalibrationCoefVan-v1.rst
@@ -0,0 +1,83 @@
+.. algorithm::
+
+.. summary::
+
+.. alias::
+
+.. properties::
+
+Description
+-----------
+
+Algorithm creates a workspace with detector sensitivity correction coefficients using the given Vanadium workspace. The correction coefficients are calculated as follows.
+
+1. Calculate the Debye-Waller factor according to Sears and Shelley *Acta Cryst. A* **47**, 441 (1991):
+
+ :math:`D_i = \exp\left(-B_i\cdot\frac{4\pi\sin\theta_i}{\lambda^2}\right)`
+
+ :math:`B_i = \frac{3\hbar^2\cdot 10^{20}}{2m_VkT_m}\cdot J(y)`
+
+ where :math:`J(y) = 0.5` if :math:`y < 10^{-3}`, otherwise
+
+ :math:`J(y) = \int_0^1 x\cdot\mathrm{coth}\left(\frac{x}{2y}\right)\,\mathrm{d}x`
+
+ where :math:`y=T/T_m` is the ratio of the temperature during the experiment :math:`T` to the Debye temperature :math:`T_m = 389K`, :math:`m_V` is the Vanadium atomic mass (in kg) and :math:`\theta_i` is the polar angle of the i-th detector.
+
+.. warning::
+
+ If sample log *temperature* is not present in the given Vanadium workspace or temperature is set to an invalid value, T=293K will be taken for the Debye-Waller factor calculation. Algorithm will produce warning in this case.
+
+2. Perform Gaussian fit of the data to find out the position of the peak centre and FWHM. These values are used to calculate sum :math:`S_i` as
+
+ :math:`S_i = \sum_{x = x_C - 3\,\mathrm{fwhm}}^{x_C + 3\,\mathrm{fwhm}} Y_i(x)`
+
+ where :math:`x_C` is the peak centre position and :math:`Y_i(x)` is the coresponding to :math:`x` :math:`Y` value for i-th detector.
+
+3. Finally, the correction coefficients :math:`K_i` are calculated as
+
+ :math:`K_i = D_i\times S_i`
+
+Workspace containing these correction coefficients is created as an output and can be used as a RHS workspace in :ref:`algm-Divide` to apply correction to the LHS workspace.
+
+.. note::
+
+ If gaussian fit fails, algorithm terminates with an error message. The error message contains name of the workspace and detector number.
+
+Restrictions on the input workspace
+###################################
+
+The valid input workspace:
+
+- must have an instrument set
+- must have a *wavelength* sample log
+
+
+Usage
+-----
+
+**Example**
+
+.. testcode:: ExComputeCalibrationCoefVan
+
+ # load Vanadium data
+ wsVana = LoadMLZ(Filename='TOFTOFTestdata.nxs')
+ # calculate correction coefficients
+ wsCoefs = ComputeCalibrationCoefVan(wsVana)
+ print 'Spectrum 4 of the output workspace is filled with: ', round(wsCoefs.readY(999)[0])
+
+ # wsCoefs can be used as rhs with Divide algorithm to apply correction to the data
+ wsCorr = wsVana/wsCoefs
+ print 'Spectrum 4 of the input workspace is filled with: ', round(wsVana.readY(999)[0], 1)
+ print 'Spectrum 4 of the corrected workspace is filled with: ', round(wsCorr.readY(999)[0], 5)
+
+Output:
+
+.. testoutput:: ExComputeCalibrationCoefVan
+
+ Spectrum 4 of the output workspace is filled with: 6596.0
+ Spectrum 4 of the input workspace is filled with: 1.0
+ Spectrum 4 of the corrected workspace is filled with: 0.00015
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst b/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
index 904b8dd2a5ccd21368da10509b6c936c4aa5fe42..1d88cdd45e69e58036d500ee26a3af2f5b079de6 100644
--- a/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
+++ b/docs/source/algorithms/ConvertCWSDExpToMomentum-v1.rst
@@ -19,18 +19,22 @@ In this algorithm's name, ConvertCWSDToMomentum, *CW* stands for constant wave
This algorithm takes ??? as inputs.
Futhermore, the unit of the output matrix workspace can be converted to
-momentum transfer (:math:`Q`).
+momentum transfer (Q).
Outline of algorithm
####################
-1. Create output workspace.
+1. Create output workspace
+
* Build a virtual instrument, requiring
+
- position of source
- position of sample
- detector ID, position, detector size of pixels
+
2. Read in data via table workspace
+
* From each row, (1) file name and (2) starting detector ID are read in.
* Detector position in (virtual) instrument of MDEventWorkspace is compared with the position in MatrixWorkspace
* Momentum is calcualted by goniometry values
@@ -75,8 +79,6 @@ Each MDEvent in output MDEventWorkspace contain
* Detector ID
* Run Number
-
-
Combine Experiment Into One MDEventWorkspace
--------------------------------------------
@@ -90,7 +92,7 @@ In order to integrate them into an organized data structure, i.e., *MDEventWorks
a virtual instrument is built in the algorithm.
Virtual instrument
-==================
+##################
A virtual instrument is built in the algorithm.
In this virtual instrument, the number of detectors and their position are determined
@@ -98,13 +100,13 @@ by the number of individual detector's positions in the *experiment*.
MDEventWorkspace
-================
+################
There is only one *virtual* instrument and *N* ExperimentInfo.
*N* is the total number of experiment points in the *experiment*.
Inconsistency between using virtual instrument and copying instrument
-=====================================================================
+#####################################################################
It is found that the results, i.e., the peak's position in sample-momentum
space, by FindPeaksMD, are different betweent the MDEventWorkspaces
@@ -145,7 +147,7 @@ with 2D angular detector.
Usage
-----
-**Example - convert an HB3A's experiment to MDWorkspace in sample momentum workspae and creating virtual instrument.:**
+**Example - convert an HB3A's experiment to MDWorkspace in sample momentum workspae and creating virtual instrument**
.. testcode:: ExConvertHB3AToMDVirtualInstrument
diff --git a/docs/source/algorithms/LoadEventAndCompress-v1.rst b/docs/source/algorithms/LoadEventAndCompress-v1.rst
index 904f90502164953738e1a6948991f082077e233c..62a3f3d65ff40e21572ce2ba45219dfb24bfb24a 100644
--- a/docs/source/algorithms/LoadEventAndCompress-v1.rst
+++ b/docs/source/algorithms/LoadEventAndCompress-v1.rst
@@ -41,6 +41,44 @@ download due to their size. They can however be downloaded using these links:
PG3_9830_event = LoadEventAndCompress(Filename='PG3_9830_event.nxs',
MaxChunkSize=1.)
+**Example - Usage with MPI**
+
+Create a python driver script called test_mpi.py
+
+.. code-block:: python
+
+ from mantid.simpleapi import *
+ import mantid
+ if AlgorithmFactory.exists('GatherWorkspaces'):
+ HAVE_MPI = True
+ from mpi4py import MPI
+ mpiRank = MPI.COMM_WORLD.Get_rank()
+ mpiSize = MPI.COMM_WORLD.Get_size()
+ else:
+ HAVE_MPI = False
+ mpiRank = 0 # simplify if clauses
+ mpiSize = 1 # simplify if clauses
+
+ wksp = LoadEventAndCompress(Filename="PG3_2538_event.nxs")
+ print "Rank = ", mpiRank, "Number of Events = ", wksp.getNumberEvents()
+ if mpiRank == 0:
+ reduce = AlignAndFocusPowder(InputWorkspace=wksp, CalFileName='PG3_calibrate_d2538_2014_05_13.cal', Params='0.5,0.01,2')
+ SaveNexus(reduce,Filename=str(mpiSize)+"tasks.nxs")
+
+And run it using the following commands
+
+.. code-block::
+
+ $ module load mpi/openmpi-x86_64
+ $ export LD_PRELOAD=/usr/lib64/openmpi/lib/libmpi.so
+ $ mpirun -np 8 mantidpython test_mpi.py
+
+to run without mpi is simply
+
+.. code-block::
+
+ $ mantidpython test_mpi.py
+
.. categories::
.. sourcelink::
diff --git a/docs/source/algorithms/MuonCalculateAsymmetry-v1.rst b/docs/source/algorithms/MuonCalculateAsymmetry-v1.rst
index 1b977a1084e9a7272aefb2610287611cb6e22440..1bbd806a20d33affe4a25d1cc4f652faa373e3d0 100644
--- a/docs/source/algorithms/MuonCalculateAsymmetry-v1.rst
+++ b/docs/source/algorithms/MuonCalculateAsymmetry-v1.rst
@@ -57,7 +57,7 @@ Output:
.. testcode:: ExGroupAsymmetryMultiperiod
y1 = [100,50,10]
- y2 = [ 50,25, 5]
+ y2 = [150,20,1]
x = [1,2,3]
input1 = CreateWorkspace(x, y1)
@@ -75,7 +75,7 @@ Output:
.. testoutput:: ExGroupAsymmetryMultiperiod
- Output: [ 0.1524242 -0.0916425 -0.71360777]
+ Output: [-0.28634067 0.60594273 0.26255546]
.. categories::
diff --git a/docs/source/concepts/DiffractionCalibrationWorkspace.rst b/docs/source/concepts/DiffractionCalibrationWorkspace.rst
index 58ee3f066f1239d1014fabe0b5b590fe423205f9..105e6e31562877adb9521585cdb43bf2205a28ff 100644
--- a/docs/source/concepts/DiffractionCalibrationWorkspace.rst
+++ b/docs/source/concepts/DiffractionCalibrationWorkspace.rst
@@ -57,3 +57,5 @@ various parameters on an instrument view.
* ``offset`` (double array) not used. Value of the legacy calibration file.
The `group` information will still be extracted into separate `GroupingWorkspace` and `MaskWorkspace`.
+
+.. categories:: Concepts
diff --git a/docs/source/concepts/MDNorm.rst b/docs/source/concepts/MDNorm.rst
index 1a1fdf7a1e8cda9fd304ef831f7c0537bcf981d6..8f2d64ba4430c6a34de7cd74f4a404caf449b819 100644
--- a/docs/source/concepts/MDNorm.rst
+++ b/docs/source/concepts/MDNorm.rst
@@ -158,4 +158,6 @@ Current implementation
As of release 3.3, the normalization can be calculated for single crystal
diffraction (:ref:`MDNormSCD <algm-MDNormSCD>`)
and single crystal direct geometry inelastic scattering
-(:ref:`MDNormDirectSC <algm-MDNormDirectSC>`).
+(:ref:`MDNormDirectSC <algm-MDNormDirectSC>`).
+
+.. categories:: Concepts
diff --git a/docs/source/concepts/Properties.rst b/docs/source/concepts/Properties.rst
index 3ea0cb965e0ad77b4b0a782ffb444d607a7fd356..71d8ab02a89f8b938f78a4585fec228801795fec 100644
--- a/docs/source/concepts/Properties.rst
+++ b/docs/source/concepts/Properties.rst
@@ -176,8 +176,7 @@ In addition to the above, if used, Workspace properties also have a
built in validator that requires that input workspaces exist and are of
the correct type and that output workspaces have a name set.
-For more details on using validators, see the
-`PropertyAlgorithm <https://github.com/mantidproject/mantid/blob/master/Code/Mantid/Framework/UserAlgorithms/PropertyAlgorithm.cpp>`__
+For more details on using validators, see the :ref:`PropertyAlgorithm <algm-PropertyAlgorithm>`
example or the full documentation for the individual validators (linked
above).
@@ -186,4 +185,4 @@ to implement the IValidator interface.
-.. categories:: Concepts
\ No newline at end of file
+.. categories:: Concepts
diff --git a/docs/source/interfaces/HFIR_4Circle_Reduction.rst b/docs/source/interfaces/HFIR_4Circle_Reduction.rst
new file mode 100644
index 0000000000000000000000000000000000000000..01c42636b87472ebfb13e637f5a3ceb0597b8c99
--- /dev/null
+++ b/docs/source/interfaces/HFIR_4Circle_Reduction.rst
@@ -0,0 +1,116 @@
+HFIR Single Crystal Reduction Interface
+=======================================
+
+.. contents:: Table of Contents
+ :local:
+
+Overview
+--------
+
+HFIR single crystalreduction interface is a GUI to download, view and reduce data from
+HFIR's four-circle single crystal diffractometer in SPICE format.
+
+
+Introduction of Tabs
+--------------------
+
+ 1. **Setup and Data Access**: Configure the instrument name, data server URL and directories.
+
+ - Configure the instrument name;
+ - Set up and test HB3A data server's URL;
+ - Configure the directory to save raw data;
+ - Configure the directory to save working result;
+ - Download data from server;
+
+ 2. **View Raw Data**: View 2D image of counts on detector of one measurement.
+
+ - Plot the counts of the 256 by 256 2D detector;
+
+ 3. **Calculate UB**: Calculate UB matrix.
+
+ - Find peak in one measurement;
+ - Option to load Miller index directly from SPICE file;
+ - Calculate UB matrix;
+ - Re-index the peaks;
+
+ 4. **Merge Scan**: Merge all the measurements in a scan.
+
+ - Merge all measuring points in a scan to an MDEventWorkspace in HKL-frame or Q-sample-frame;
+ - Allow various ways to set up UB matrix
+
+ 5. **Refine UB**: Refine UB matrix
+
+ - Disabled becaues it is in development still;
+
+ 6. **Peak Integration**: Integrate peaks
+
+ - Disabled because it is still in development.
+
+Use Cases
+---------
+
+Here are some use cases that can be used as examples.
+
+
+Workflow to calculate UB matrix
++++++++++++++++++++++++++++++++
+
+Here is a typical use case to calculate UB matrix
+
+ 1. User specifies *Experiment* and pushes button *Set*
+
+ 2. User enters tab *View Raw Data*
+
+ 3. User inputs scan number and list all the measuring points
+
+ 4. User views all the measurements
+
+ 5. User finds out the measurement with the strongest reflection and push button use
+
+ 6. GUI shifts to tab *Calculate UB* automatically
+
+ 7. User pushes button *Find Peak* with checking *Load HKL from file*
+
+ 8. GUI finds the peak center and load HKL
+
+ 9. User pushes button *Add peak* to add the peak to table
+
+ 10. User repeats step 2 to 9 to add other peaks
+
+ 11. User select the peaks that are linearly independent and pushes *Calcualte UB*
+
+ 12. GUI calculates UB matrix and show the result
+
+ 13. User may push *Index peak* to use the calculated UB matrix to index peaks in the table to check UB matrix.
+
+
+Workflow to merge measurements in scan
+++++++++++++++++++++++++++++++++++++++
+
+Here is a typical use case to merge all the measuring points (Pt.) in a scan.
+
+ 1. User specifies *Experiment* and pushes button *Set*
+
+ 2. User enters tab *Merge Scan*
+
+ 3. User specifies the UB matrix either by *From tab Calculate UB* or by entering the values to text editor
+
+ 4. User pushes button *Set*.
+
+ 5. User specifies the frame in which the merged data will be in. If the target frame is Q-Sample-Sapce, then there is
+ no need to specify UB matrix;
+
+ 6. User specifies the scan numbers and push button *Add*;
+
+ 7. User specifies the base name for the output MDEventWorkspaces;
+
+ 8. User pushes button *Process*;
+
+ 9. User goes to MantidPlot to view the merged scan by SliceView or Vates.
+
+
+
+Limitation
+----------
+
+- HFIR single crystal reduction GUI supports for instrument HB3A only from release 3.5.0 and nightly.
diff --git a/docs/sphinxext/mantiddoc/directives/algorithm.py b/docs/sphinxext/mantiddoc/directives/algorithm.py
index e01645c182f245813f77a10fedcaa153b782c8d7..9333d680eea9274d2bf3de4d7f6ed1b82a5d56f6 100644
--- a/docs/sphinxext/mantiddoc/directives/algorithm.py
+++ b/docs/sphinxext/mantiddoc/directives/algorithm.py
@@ -202,7 +202,7 @@ class AlgorithmDirective(AlgorithmBaseDirective):
#------------------------------------------------------------------------------------------------------------
-def html_collect_pages(app):
+def html_collect_pages(dummy_app):
"""
Write out unversioned algorithm pages that redirect to the highest version of the algorithm
"""
diff --git a/docs/sphinxext/mantiddoc/directives/properties.py b/docs/sphinxext/mantiddoc/directives/properties.py
index 0531ada285c35b0231d90c388590851163e635ad..2e14a854077bea111e82ccfd43608175a5733b77 100644
--- a/docs/sphinxext/mantiddoc/directives/properties.py
+++ b/docs/sphinxext/mantiddoc/directives/properties.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from mantiddoc.directives.base import AlgorithmBaseDirective
import string
diff --git a/docs/sphinxext/mantiddoc/directives/sourcelink.py b/docs/sphinxext/mantiddoc/directives/sourcelink.py
index f60bee49b5fc22ad5029399456c5cba1190f679b..1e436b1f71b441e1c1e965677e7e8391578d7249 100644
--- a/docs/sphinxext/mantiddoc/directives/sourcelink.py
+++ b/docs/sphinxext/mantiddoc/directives/sourcelink.py
@@ -150,7 +150,7 @@ class SourceLinkDirective(AlgorithmBaseDirective):
builddir = os.path.join(builddir, "..", "..")
builddir = os.path.abspath(builddir)
- for dirName, subdirList, fileList in os.walk(self.source_root):
+ for dirName, dummy_subdirList, fileList in os.walk(self.source_root):
if dirName.startswith(builddir):
continue # don't check or add to the cache
for fname in fileList:
@@ -186,29 +186,31 @@ class SourceLinkDirective(AlgorithmBaseDirective):
suggested_path = "os_agnostic_path_to_file_from_Code/Mantid"
if len(valid_ext_list) == 0:
raise SourceLinkError("No file possibilities for " + file_name + " have been found\n" +
- "Please specify a better one using the :filename: opiton or use the " + str(self.file_types.keys()) + " options\n" +
- "e.g. \n" +
- ".. sourcelink:\n" +
- " :" + self.file_types.keys()[0] + ": " + suggested_path + "\n "+
- "or \n" +
- ".. sourcelink:\n" +
- " :filename: " + file_name)
+ "Please specify a better one using the :filename: opiton or use the " +
+ str(self.file_types.keys()) + " options\n" +
+ "e.g. \n" +
+ ".. sourcelink:\n" +
+ " :" + self.file_types.keys()[0] + ": " + suggested_path + "\n "+
+ "or \n" +
+ ".. sourcelink:\n" +
+ " :filename: " + file_name)
#if the have a cpp we should also have a h
if ("cpp" in valid_ext_list) or ("h" in valid_ext_list):
if ("cpp" not in valid_ext_list) or ("h" not in valid_ext_list):
raise SourceLinkError("Only one of .h and .cpp found for " + file_name + "\n" +
- "valid files found for " + str(valid_ext_list) + "\n" +
- "Please specify the missing one using an " + str(self.file_types.keys()) + " option\n" +
- "e.g. \n" +
- ".. sourcelink:\n" +
- " :" + self.file_types.keys()[0] + ": " + suggested_path)
+ "valid files found for " + str(valid_ext_list) + "\n" +
+ "Please specify the missing one using an " +
+ str(self.file_types.keys()) + " option\n" +
+ "e.g. \n" +
+ ".. sourcelink:\n" +
+ " :" + self.file_types.keys()[0] + ": " + suggested_path)
return
def output_path_to_page(self, filepath, extension):
"""
Outputs the source link for a file to the rst page
"""
- dirName,fName = os.path.split(filepath)
+ dummy_dirName,fName = os.path.split(filepath)
self.add_rst(self.file_types[extension] + ": `" + fName + " <" + self.convert_path_to_github_url(filepath) + ">`_\n\n")
return
diff --git a/docs/sphinxext/mantiddoc/doctest.py b/docs/sphinxext/mantiddoc/doctest.py
index e4364825320559fc06647688164ba4025b609d72..d6d176e0159c852380fc41e67e5d3993c89f0b7d 100644
--- a/docs/sphinxext/mantiddoc/doctest.py
+++ b/docs/sphinxext/mantiddoc/doctest.py
@@ -198,7 +198,7 @@ class TestCaseReport(object):
@property
def passed(self):
- return (self.failure_descr == "")
+ return self.failure_descr == ""
@property
def failed(self):
@@ -309,7 +309,7 @@ class DocTestOutputParser(object):
% text[1])
results = results[2:] # trim off top two lines of header information
maintests, cleanup = self.__split_on_cleanup(results)
- overall_success = not (maintests[0] == FAILURE_MARKER)
+ overall_success = not maintests[0] == FAILURE_MARKER
if overall_success:
testcases = self.__parse_success(fullname, maintests)
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 7c00c508283118881ab92f0d7c8e6b079bc1f0f3..7cd45300f74869139a60cf613343c6613fe322d6 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -6,6 +6,7 @@ add_subdirectory(Interface/ui)
add_subdirectory(lib1to2/gui)
add_subdirectory(PyChop)
add_subdirectory(TofConverter)
+add_subdirectory(HFIR_4Circle_Reduction)
# Chain all required interface custom targets into CompilePyUI
add_custom_target(CompilePyUI DEPENDS
@@ -15,6 +16,7 @@ add_custom_target(CompilePyUI DEPENDS
CompileUITofConverter
CompileUIUI
CompileUILib1To2
+ CompileUIHFIR_4Circle_Reduction
)
set ( TEST_PY_FILES
diff --git a/scripts/HFIR_4Circle_Reduction.py b/scripts/HFIR_4Circle_Reduction.py
new file mode 100644
index 0000000000000000000000000000000000000000..89742c6bfa9f75bb50d994cf3148f7d9e1c84476
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction.py
@@ -0,0 +1,17 @@
+#pylint: disable=invalid-name
+from HFIR_4Circle_Reduction import reduce4circleGUI
+from PyQt4 import QtGui
+import sys
+
+def qapp():
+ if QtGui.QApplication.instance():
+ _app = QtGui.QApplication.instance()
+ else:
+ _app = QtGui.QApplication(sys.argv)
+ return _app
+
+app = qapp()
+
+reducer = reduce4circleGUI.MainWindow() #the main ui class in this file is called MainWindow
+reducer.show()
+app.exec_()
diff --git a/scripts/HFIR_4Circle_Reduction/CMakeLists.txt b/scripts/HFIR_4Circle_Reduction/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67fe46df205d951ff83380c933f71c88d5325604
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/CMakeLists.txt
@@ -0,0 +1,8 @@
+include(UiToPy)
+
+# List of UIs to Auto convert
+set( UI_FILES
+ MainWindow.ui
+)
+
+UiToPy( UI_FILES CompileUIHFIR_4Circle_Reduction)
diff --git a/scripts/HFIR_4Circle_Reduction/MainWindow.ui b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
new file mode 100644
index 0000000000000000000000000000000000000000..4f7fa462e7008c7cf9e167e822ad5b0b47996aca
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/MainWindow.ui
@@ -0,0 +1,2312 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>1292</width>
+ <height>783</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>4-Circle Reduction</string>
+ </property>
+ <widget class="QWidget" name="centralwidget">
+ <layout class="QHBoxLayout" name="horizontalLayout_11">
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_General">
+ <item>
+ <widget class="QLabel" name="label_exp">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Experiment</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_exp">
+ <property name="minimumSize">
+ <size>
+ <width>40</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setExp">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_11">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_15">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Unit Cell</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_16">
+ <property name="text">
+ <string>a</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_a">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_23">
+ <property name="text">
+ <string>b</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_b">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_24">
+ <property name="text">
+ <string>c</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_c">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_25">
+ <property name="text">
+ <string>alpha</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_alpha">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_26">
+ <property name="text">
+ <string>beta</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_beta">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_27">
+ <property name="text">
+ <string>gamma</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_gamma">
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_Tab">
+ <item>
+ <widget class="QTabWidget" name="tabWidget">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="currentIndex">
+ <number>0</number>
+ </property>
+ <widget class="QWidget" name="tab">
+ <attribute name="title">
+ <string>Setup && Data Access</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_5">
+ <item row="1" column="0">
+ <widget class="QTextEdit" name="textEdit">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="readOnly">
+ <bool>true</bool>
+ </property>
+ <property name="html">
+ <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;">
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-weight:600;">1. Configure the data reduction</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(a) Do not modify ServerURL unless necessary;</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(b) Click 'Apply' to check internet connection and directories;</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(c) If 'Time out' is popped out, try to click 'Apply' again. Server may not be able to respond promptly.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:10pt; font-style:italic;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-weight:600;">2. Start to reduce data</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:10pt; font-style:italic;">(a) Set</span><span style=" font-size:10pt;"> Experiment</span></p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="0">
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Configuration</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_11">
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_testURLs">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>200</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Test</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QPushButton" name="pushButton_browseLocalDataDir">
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <spacer name="horizontalSpacer">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_localSpiceDir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory for local data storage</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_instrument">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Instrument</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_dir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory for local data storage</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Data Directory</string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QComboBox" name="comboBox_instrument">
+ <item>
+ <property name="text">
+ <string>HB3A</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_useDefaultDir">
+ <property name="font">
+ <font>
+ <pointsize>10</pointsize>
+ </font>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Use default set up</p><p><br/></p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Load Default</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="1">
+ <widget class="QLineEdit" name="lineEdit_workDir">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory to save outcome of the data reduction</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_url">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_url">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>URL of the http server to download HB3A data</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Server URL</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPushButton" name="pushButton_browseWorkDir">
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_2">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>1</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>140</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Directory to save outcome of the data reduction</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Working Direcotry</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="2">
+ <widget class="QPushButton" name="pushButton_applySetup">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Apply</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QGroupBox" name="groupBox_2">
+ <property name="title">
+ <string>Data Download</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_12">
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_browseLocalCache">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Browse</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Scans List</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QComboBox" name="comboBox_mode">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Mode &quot;download&quot;: download data to local disk;</p><p>Mode &quot;http server only&quot;: download data to cache, process and delete cached data upon returning</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>Download Complete Experiment</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Download Selected Scans</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_localSrcDir">
+ <property name="toolTip">
+ <string><html><head/><body><p>Cache on local disk. The dowloaded data will be saved to here. </p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_datamode">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Download Mode</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_4">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>140</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Destination</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="6">
+ <spacer name="horizontalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Minimum</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_downloadExpData">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p><span style=" font-weight:400;">Download scans specified by 'Scans List'; </span></p><p><span style=" font-weight:400;">If 'Scans List' is empty, then the complete experiment data will be downloaded</span></p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Download</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_downloadScans"/>
+ </item>
+ <item row="2" column="2">
+ <widget class="QPushButton" name="pushButton_ListScans">
+ <property name="text">
+ <string>List Scans</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <spacer name="verticalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_4">
+ <attribute name="title">
+ <string>View Raw Data</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_9">
+ <item row="0" column="0">
+ <layout class="QGridLayout" name="gridLayout_3">
+ <item row="0" column="3">
+ <layout class="QVBoxLayout" name="verticalLayout_5">
+ <item>
+ <layout class="QGridLayout" name="gridLayout"/>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_3">
+ <property name="title">
+ <string>Scan</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_run">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>10</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>10000</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setScanInfo">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_showPtList">
+ <property name="text">
+ <string>List Pt.</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="Line" name="line">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_4">
+ <property name="title">
+ <string> Pt</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_rawDataPtNo">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>1000</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_plotRawPt">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>80</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Plot</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_usePt4UB">
+ <property name="toolTip">
+ <string><html><head/><body><p>Use this peak to calcualate UB matrix</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Use</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Minimum</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_8">
+ <item>
+ <widget class="QPushButton" name="pushButton_prevPtNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>30</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>40</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Previous Pt. No</p></body></html></string>
+ </property>
+ <property name="text">
+ <string><---|</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_7">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>5</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_nextPtNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>30</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>40</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>|--></string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="0" column="0">
+ <widget class="MplGraphicsView" name="graphicsView">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_2">
+ <attribute name="title">
+ <string>Calculate UB</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_6">
+ <item row="0" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_4">
+ <item>
+ <widget class="QGroupBox" name="groupBox_7">
+ <property name="title">
+ <string>Add Peak</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_scanNo">
+ <property name="text">
+ <string>Scan Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="8">
+ <widget class="QLineEdit" name="lineEdit_H">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>40</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_PtNo">
+ <property name="text">
+ <string>Pt Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="12">
+ <widget class="QLineEdit" name="lineEdit_sampleQy">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="11">
+ <widget class="QLabel" name="label_11">
+ <property name="text">
+ <string>K</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="13">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string>L</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="8">
+ <widget class="QLineEdit" name="lineEdit_sampleQx">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="6">
+ <widget class="QLabel" name="label_7">
+ <property name="text">
+ <string> Q-Sample </string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLineEdit" name="lineEdit_ptNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="11">
+ <widget class="QLabel" name="label_9">
+ <property name="text">
+ <string>Y</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="14">
+ <widget class="QLineEdit" name="lineEdit_sampleQz">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>120</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="7">
+ <widget class="QLabel" name="label_8">
+ <property name="text">
+ <string>X</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_scanNumber">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="12">
+ <widget class="QLineEdit" name="lineEdit_K">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="14">
+ <widget class="QLineEdit" name="lineEdit_L">
+ <property name="maximumSize">
+ <size>
+ <width>60</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="7">
+ <widget class="QLabel" name="label_12">
+ <property name="text">
+ <string>H</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="13">
+ <widget class="QLabel" name="label_10">
+ <property name="text">
+ <string>Z</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <spacer name="horizontalSpacer_4">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="0" column="6">
+ <widget class="QLabel" name="label_31">
+ <property name="text">
+ <string>Miller Index</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <widget class="QPushButton" name="pushButton_findPeak">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Find Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="4">
+ <widget class="QCheckBox" name="checkBox_loadHKLfromFile">
+ <property name="font">
+ <font>
+ <pointsize>9</pointsize>
+ </font>
+ </property>
+ <property name="text">
+ <string>Load HKL from file</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_7">
+ <item>
+ <widget class="UBMatrixPeakTable" name="tableWidget_peaksCalUB"/>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_8">
+ <item>
+ <widget class="QPushButton" name="pushButton_addPeakToCalUB">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Add Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_roundHKLInt">
+ <property name="font">
+ <font>
+ <pointsize>9</pointsize>
+ </font>
+ </property>
+ <property name="text">
+ <string>RoundHKL to int</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_11">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_deleteUBPeak">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>200</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Delete</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_clearUBPeakTable">
+ <property name="text">
+ <string>Clear</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_7">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_13">
+ <item>
+ <widget class="QLabel" name="label_32">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="font">
+ <font>
+ <pointsize>14</pointsize>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>UB Matrix</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_6">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_ubMatrix">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>360</width>
+ <height>0</height>
+ </size>
+ </property>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_12">
+ <item>
+ <widget class="QPushButton" name="pushButton_calUB">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Calculate UB</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_8">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_acceptUB">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Accept</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_9">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_8">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_9">
+ <item>
+ <widget class="QPushButton" name="pushButton_indexUBPeaks">
+ <property name="minimumSize">
+ <size>
+ <width>100</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>100</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="text">
+ <string>Index Peak</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_12">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_resetPeakHKLs">
+ <property name="text">
+ <string>Reset HKL</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_advsetup">
+ <attribute name="title">
+ <string>Merge Scan</string>
+ </attribute>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QGroupBox" name="groupBox_5">
+ <property name="title">
+ <string>UB Matrix</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_13">
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_ubSiceView">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>150</height>
+ </size>
+ </property>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <item row="0" column="0">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ <item row="1" column="1">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ <item row="2" column="2">
+ <property name="text">
+ <string>1</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_13">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <layout class="QGridLayout" name="gridLayout_4">
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_3">
+ <property name="text">
+ <string>From tab 'Caclulate UB'</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QRadioButton" name="radioButton_ubFromTab1">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <spacer name="horizontalSpacer_9">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Preferred</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item row="2" column="0">
+ <widget class="QRadioButton" name="radioButton_ubFromTab3">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLabel" name="label_28">
+ <property name="text">
+ <string>From tab 'Refine UB'</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPlainTextEdit" name="plainTextEdit_ubInput">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_15">
+ <item>
+ <widget class="QRadioButton" name="radioButton_ubFromList">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_15">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_14">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Ignored</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_setUBSliceView">
+ <property name="text">
+ <string>Set</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="verticalSpacer_10">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="groupBox_6">
+ <property name="title">
+ <string>Process Data</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_14">
+ <item>
+ <layout class="QGridLayout" name="gridLayout_10">
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_29">
+ <property name="toolTip">
+ <string><html><head/><body><p>For MDEventsWorkspace with merged runs</p><p><br/></p><p>For example:</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Base Workspace Name</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_30">
+ <property name="text">
+ <string>Scans List</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_listScansSliceView"/>
+ </item>
+ <item row="0" column="2">
+ <widget class="QPushButton" name="pushButton_addScanSliceView">
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QLineEdit" name="lineEdit_baseMergeMDName">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="comboBox_mergeScanFrame">
+ <property name="minimumSize">
+ <size>
+ <width>140</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="toolTip">
+ <string><html><head/><body><p>Type of frame that the final merged scan will be in.</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>HKL-Space</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Q-Sample-Space</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_10">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeType">
+ <enum>QSizePolicy::Expanding</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="2">
+ <widget class="QPushButton" name="pushButton_process4SliceView">
+ <property name="font">
+ <font>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="text">
+ <string>Process</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="ProcessTableWidget" name="tableWidget_sliceViewProgress">
+ <property name="toolTip">
+ <string><html><head/><body><p>? columns: </p><p><br/></p><p>1. Scan number</p><p>2. Number of Pts.</p><p>3. Status: </p><p>(a) done</p><p>(b) error with error message</p><p>(c) on-going</p><p>(d) empty as not yet</p></body></html></string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_3">
+ <attribute name="title">
+ <string>Refine UB</string>
+ </attribute>
+ <layout class="QGridLayout" name="gridLayout_8">
+ <item row="0" column="0">
+ <layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_14">
+ <item>
+ <widget class="QLabel" name="label_14">
+ <property name="text">
+ <string>Scan</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_scanRefineUB">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Maximum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label_13">
+ <property name="text">
+ <string>Pt.</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLineEdit" name="lineEdit_ptRefineUB">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_addToRefine">
+ <property name="toolTip">
+ <string><html><head/><body><p>Add a data point or data points (defined by scan number and pt number) to the list to refine UB matrix; </p><p><br/></p><p>Scan number can be a list of integers;</p><p><br/></p><p>Pt number can be empty such that all Pt. of that scan will be searched for peak and then used to refine UB matrix</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Add</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_addAllRefineUB">
+ <property name="text">
+ <string>Add All</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_15">
+ <item>
+ <widget class="UBMatrixTable" name="tableWidget_refinedUB">
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <row>
+ <property name="text">
+ <string/>
+ </property>
+ </row>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ <column>
+ <property name="text">
+ <string/>
+ </property>
+ </column>
+ </widget>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_7"/>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_10">
+ <item>
+ <widget class="QPushButton" name="pushButton_acceptRefinedUB">
+ <property name="text">
+ <string>Accept</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_resetRefinedUB">
+ <property name="text">
+ <string>Reset</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QGridLayout" name="gridLayout_7">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_17">
+ <property name="text">
+ <string>a</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_19">
+ <property name="text">
+ <string>c</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="4">
+ <widget class="QLabel" name="label_21">
+ <property name="text">
+ <string>beta</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="label_18">
+ <property name="text">
+ <string>b</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLabel" name="label_20">
+ <property name="text">
+ <string>alpha</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <widget class="QLabel" name="label_22">
+ <property name="text">
+ <string>gamma</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_bUnitCell"/>
+ </item>
+ <item row="1" column="2">
+ <widget class="QLineEdit" name="lineEdit_cUnitCell"/>
+ </item>
+ <item row="1" column="3">
+ <widget class="QLineEdit" name="lineEdit_alphaUnitCell"/>
+ </item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="lineEdit_bError"/>
+ </item>
+ <item row="1" column="4">
+ <widget class="QLineEdit" name="lineEdit_betaUnitCell"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLineEdit" name="lineEdit_aUnitCell"/>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLineEdit" name="lineEdit_cError"/>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLineEdit" name="lineEdit_aError"/>
+ </item>
+ <item row="2" column="3">
+ <widget class="QLineEdit" name="lineEdit_alphaError"/>
+ </item>
+ <item row="2" column="4">
+ <widget class="QLineEdit" name="lineEdit_betaError"/>
+ </item>
+ <item row="1" column="5">
+ <widget class="QLineEdit" name="lineEdit_gammaUnitCell"/>
+ </item>
+ <item row="2" column="5">
+ <widget class="QLineEdit" name="lineEdit_gammaError"/>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="0">
+ <spacer name="verticalSpacer_3">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QWidget" name="tab_indexPeak">
+ <attribute name="title">
+ <string>Peak Integration</string>
+ </attribute>
+ <layout class="QVBoxLayout" name="verticalLayout_11">
+ <item>
+ <layout class="QGridLayout" name="gridLayout_13">
+ <item row="1" column="6">
+ <widget class="QCheckBox" name="checkBox_adaptQBkgd">
+ <property name="text">
+ <string>Adaptive Q Background</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLineEdit" name="lineEdit_scanIntegratePeak">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QCheckBox" name="checkBox_cylinder">
+ <property name="text">
+ <string>Cylinder</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="3">
+ <widget class="QLineEdit" name="lineEdit_bkgdInnerR"/>
+ </item>
+ <item row="1" column="5">
+ <widget class="QLineEdit" name="lineEdit_bkgdOuterR"/>
+ </item>
+ <item row="2" column="4">
+ <widget class="QLabel" name="label_36">
+ <property name="text">
+ <string>Percent Background</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="7">
+ <widget class="QCheckBox" name="checkBox_integrateOnEdge">
+ <property name="text">
+ <string>Integrate on Edge</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_5">
+ <property name="text">
+ <string>Scan Number</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_34">
+ <property name="text">
+ <string>Peak Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLineEdit" name="lineEdit_ptNumListIntPeak"/>
+ </item>
+ <item row="2" column="7">
+ <widget class="QComboBox" name="comboBox_cylinderIntOption"/>
+ </item>
+ <item row="0" column="7">
+ <widget class="QPushButton" name="pushButton_integratePeak">
+ <property name="text">
+ <string>Integrate Peaks</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="5">
+ <widget class="QLineEdit" name="lineEdit_cylinderBkgdPercent"/>
+ </item>
+ <item row="1" column="4">
+ <widget class="QLabel" name="label_35">
+ <property name="text">
+ <string>Background Outer Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="5">
+ <widget class="QComboBox" name="comboBox_3">
+ <property name="toolTip">
+ <string><html><head/><body><p>Choose the name of the tab, in which the UB matrix is used to convert signals to HKL frame.</p></body></html></string>
+ </property>
+ <item>
+ <property name="text">
+ <string>Calculate UB</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Merge Scan</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Refine UB</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="2" column="6">
+ <widget class="QComboBox" name="comboBox_cylinderProfile">
+ <item>
+ <property name="text">
+ <string>Gaussian</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLabel" name="label_39">
+ <property name="text">
+ <string>Cylinder Length</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QLabel" name="label_37">
+ <property name="text">
+ <string>Background Inner Radius</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <widget class="QLineEdit" name="lineEdit_cylinderLength"/>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="label_33">
+ <property name="text">
+ <string>Pt Numbers</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="lineEdit_peakRadius"/>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <widget class="IntegratePeaksTableWidget" name="tableWidget_peakIndex"/>
+ </item>
+ </layout>
+ </widget>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QMenuBar" name="menubar">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>1292</width>
+ <height>25</height>
+ </rect>
+ </property>
+ <widget class="QMenu" name="menuFile">
+ <property name="title">
+ <string>File</string>
+ </property>
+ <addaction name="separator"/>
+ <addaction name="actionExit"/>
+ <addaction name="separator"/>
+ </widget>
+ <widget class="QMenu" name="menuTools">
+ <property name="title">
+ <string>Tools</string>
+ </property>
+ <addaction name="actionSave_Session"/>
+ <addaction name="actionLoad_Session"/>
+ <addaction name="separator"/>
+ </widget>
+ <addaction name="menuFile"/>
+ <addaction name="menuTools"/>
+ </widget>
+ <widget class="QStatusBar" name="statusbar"/>
+ <action name="actionNew">
+ <property name="text">
+ <string>New</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+N</string>
+ </property>
+ </action>
+ <action name="actionOpen">
+ <property name="text">
+ <string>Open</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+O</string>
+ </property>
+ </action>
+ <action name="actionSave">
+ <property name="text">
+ <string>Save</string>
+ </property>
+ </action>
+ <action name="actionLog">
+ <property name="text">
+ <string>Log</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+L</string>
+ </property>
+ </action>
+ <action name="actionSave_Session">
+ <property name="text">
+ <string>Save Session</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Shift+S</string>
+ </property>
+ </action>
+ <action name="actionExit">
+ <property name="text">
+ <string>Exit</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Q</string>
+ </property>
+ </action>
+ <action name="actionLoad_Session">
+ <property name="text">
+ <string>Load Session</string>
+ </property>
+ <property name="shortcut">
+ <string>Ctrl+Shift+L</string>
+ </property>
+ </action>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>MplGraphicsView</class>
+ <extends>QGraphicsView</extends>
+ <header>mplgraphicsview.h</header>
+ </customwidget>
+ <customwidget>
+ <class>UBMatrixPeakTable</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>UBMatrixTable</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>ProcessTableWidget</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ <customwidget>
+ <class>IntegratePeaksTableWidget</class>
+ <extends>QTableWidget</extends>
+ <header>hfctables.h</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/scripts/HFIR_4Circle_Reduction/NTableWidget.py b/scripts/HFIR_4Circle_Reduction/NTableWidget.py
new file mode 100644
index 0000000000000000000000000000000000000000..198725f41ef1492b822dfddb572ecb7c75b0a3aa
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/NTableWidget.py
@@ -0,0 +1,268 @@
+#pylint: disable=C0103,R0904
+# N(DAV)TableWidget
+#
+
+from PyQt4 import QtGui, QtCore
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ _fromUtf8 = lambda s: s
+
+
+class NTableWidget(QtGui.QTableWidget):
+ """
+ NdavTableWidget inherits from QTableWidget by extending the features
+ for easy application.
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ QtGui.QTableWidget.__init__(self, parent)
+
+ self._myParent = parent
+
+ self._myHeaderList = None
+ self._myColumnTypeList = None
+
+ return
+
+ def append_row(self, row_value_list, type_list=None):
+ """
+
+ :param row_value_list:
+ :return:
+ """
+ # Check input
+ assert isinstance(row_value_list, list)
+ if type_list is not None:
+ assert isinstance(type_list, list)
+ assert len(row_value_list) == len(type_list)
+ else:
+ type_list = self._myColumnTypeList
+ if len(row_value_list) != self.columnCount():
+ ret_msg = 'Input number of values (%d) is different from ' \
+ 'column number (%d).' % (len(row_value_list), self.columnCount())
+ return False, ret_msg
+ else:
+ ret_msg = ''
+
+ # Insert new row
+ row_number = self.rowCount()
+ self.insertRow(row_number)
+
+ # Set values
+ for i_col in xrange(min(len(row_value_list), self.columnCount())):
+ item = QtGui.QTableWidgetItem()
+ item.setText(_fromUtf8(str(row_value_list[i_col])))
+ item.setFlags(item.flags() & ~QtCore.Qt.ItemIsEditable)
+ if type_list[i_col] == 'checkbox':
+ self.set_check_box(row_number, i_col, False)
+ else:
+ self.setItem(row_number, i_col, item)
+ # END-FOR(i_col)
+
+ return True, ret_msg
+
+ def delete_rows(self, row_number_list):
+ """ Delete rows
+ :param row_number_list:
+ :return:
+ """
+ # Check and re-order row numbers
+ assert isinstance(row_number_list, list)
+ row_number_list.sort(reverse=True)
+
+ for row_number in row_number_list:
+ self.removeRow(row_number)
+
+ return
+
+ def get_selected_rows(self):
+ """
+
+ :return: list of row numbers that are selected
+ """
+ rows_list = list()
+ index_status = self._myColumnTypeList.index('checkbox')
+ for i_row in xrange(self.rowCount()):
+ is_checked = self.get_row_value(i_row)[index_status]
+ if is_checked:
+ rows_list.append(i_row)
+
+ return rows_list
+
+ def get_cell_value(self, row_index, col_index):
+ """
+
+ :param row_index:
+ :param col_index:
+ :return:
+ """
+ c_type = self._myColumnTypeList[col_index]
+
+ return_value = None
+ if c_type == 'checkbox':
+ # Check box
+ cell_i_j = self.cellWidget(row_index, col_index)
+ assert isinstance(cell_i_j, QtGui.QCheckBox)
+ return_value = cell_i_j.isChecked()
+ else:
+ # Regular cell
+ item_i_j = self.item(row_index, col_index)
+ assert isinstance(item_i_j, QtGui.QTableWidgetItem)
+ value = str(item_i_j.text())
+ if c_type == 'int':
+ return_value = int(value)
+ elif c_type == 'float':
+ return_value = float(value)
+
+ return return_value
+
+ def get_row_value(self, row_index):
+ """
+ :param row_index:
+ :return: list of objects
+ """
+ if row_index < 0 or row_index >= self.rowCount():
+ raise IndexError('Index of row (%d) is out of range.' % row_index)
+
+ ret_list = list()
+ for i_col in xrange(len(self._myColumnTypeList)):
+ c_type = self._myColumnTypeList[i_col]
+
+ if c_type == 'checkbox':
+ # Check box
+ cell_i_j = self.cellWidget(row_index, i_col)
+ assert isinstance(cell_i_j, QtGui.QCheckBox)
+ is_checked = cell_i_j.isChecked()
+ ret_list.append(is_checked)
+ else:
+ # Regular cell
+ item_i_j = self.item(row_index, i_col)
+ assert isinstance(item_i_j, QtGui.QTableWidgetItem)
+ value = str(item_i_j.text()).strip()
+ if len(value) > 0:
+ if c_type == 'int':
+ value = int(value)
+ elif c_type == 'float':
+ value = float(value)
+ else:
+ value = None
+
+ ret_list.append(value)
+ # END-IF-ELSE
+ # END-FOR
+
+ return ret_list
+
+ def init_setup(self, column_tup_list):
+ """ Initial setup
+ :param column_tup_list: list of 2-tuple as string (column name) and string (data type)
+ :return:
+ """
+ # Define column headings
+ num_cols = len(column_tup_list)
+
+ # Class variables
+ self._myHeaderList = list()
+ self._myColumnTypeList = list()
+
+ for c_tup in column_tup_list:
+ c_name = c_tup[0]
+ c_type = c_tup[1]
+ self._myHeaderList.append(c_name)
+ self._myColumnTypeList.append(c_type)
+
+ self.setColumnCount(num_cols)
+ self.setHorizontalHeaderLabels(self._myHeaderList)
+
+ return
+
+ def init_size(self, num_rows, num_cols):
+ """
+
+ :return:
+ """
+ self.setColumnCount(num_cols)
+ self.setRowCount(num_rows)
+
+ return
+
+ def set_check_box(self, row, col, state):
+ """ function to add a new select checkbox to a cell in a table row
+ won't add a new checkbox if one already exists
+ """
+ # Check input
+ assert isinstance(state, bool)
+
+ # Check if cellWidget exists
+ if self.cellWidget(row,col):
+ # existing: just set the value
+ self.cellWidget(row, col).setChecked(state)
+ else:
+ # case to add checkbox
+ checkbox = QtGui.QCheckBox()
+ checkbox.setText('')
+ checkbox.setChecked(state)
+
+ # Adding a widget which will be inserted into the table cell
+ # then centering the checkbox within this widget which in turn,
+ # centers it within the table column :-)
+ self.setCellWidget(row, col, checkbox)
+ # END-IF-ELSE
+
+ return
+
+ def set_value_cell(self, row, col, value=''):
+ """
+ Set value to a cell with integer, float or string
+ :param row:
+ :param col:
+ :param value:
+ :return:
+ """
+ # Check
+ if row < 0 or row >= self.rowCount() or col < 0 or col >= self.columnCount():
+ raise IndexError('Input row number or column number is out of range.')
+
+ # Init cell
+ cell_item = QtGui.QTableWidgetItem()
+ cell_item.setText(_fromUtf8(str(value)))
+ cell_item.setFlags(cell_item.flags() & ~QtCore.Qt.ItemIsEditable)
+
+ self.setItem(row, col, cell_item)
+
+ return
+
+ def update_cell_value(self, row, col, value):
+ """
+
+ :param row:
+ :param col:
+ :param value:
+ :return:
+ """
+ cell_item = self.item(row, col)
+ cell_widget = self.cellWidget(row, col)
+
+ if cell_item is not None and cell_widget is None:
+ # TableWidgetItem
+ assert isinstance(cell_item, QtGui.QTableWidgetItem)
+ if isinstance(value, float):
+ cell_item.setText(_fromUtf8('%.7f' % value))
+ else:
+ cell_item.setText(_fromUtf8(str(value)))
+ elif cell_item is None and cell_widget is not None:
+ # TableCellWidget
+ if isinstance(cell_item, QtGui.QCheckBox) is True:
+ cell_item.setChecked(value)
+ else:
+ raise TypeError('Cell of type %s is not supported.' % str(type(cell_item)))
+ else:
+ raise TypeError('Table cell (%d, %d) is in an unsupported situation!' % (row, col))
+
+ return
diff --git a/scripts/HFIR_4Circle_Reduction/__init__.py b/scripts/HFIR_4Circle_Reduction/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..04a95e8315757618d54dc05da33da722b0774d94
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/__init__.py
@@ -0,0 +1,2 @@
+#pylint: disable=invalid-name
+#pylint: disable=invalid-name
diff --git a/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py b/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py
new file mode 100644
index 0000000000000000000000000000000000000000..35dc1fe387e6bd1597eed0a9eb6c52f8c08811f8
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/fourcircle_utility.py
@@ -0,0 +1,188 @@
+#pylint: disable=W0633,too-many-branches
+__author__ = 'wzz'
+
+import os
+import urllib2
+import socket
+
+
+def check_url(url, read_lines=False):
+ """ Check whether a URL is valid
+ :param url:
+ :return: boolean, error message
+ """
+ lines = None
+ try:
+ # Access URL
+ url_stream = urllib2.urlopen(url, timeout=2)
+
+ # Read lines
+ if read_lines is True:
+ lines = url_stream.readlines()
+ except urllib2.URLError as url_error:
+ url_stream = url_error
+ except socket.timeout:
+ return False, 'Time out. Try again!'
+
+ # Return result
+ if url_stream.code in (200, 401):
+ url_good = True
+ else:
+ url_good = False
+
+ # Close connect
+ url_stream.close()
+
+ # Return
+ if read_lines is True:
+ return url_good, lines
+ if url_good is False:
+ error_message = 'Unable to access %s. Check internet access. Code %d' % (url, url_stream.code)
+ else:
+ error_message = ''
+
+ return url_good, error_message
+
+
+def get_scans_list(server_url, exp_no, return_list=False):
+ """ Get list of scans under one experiment
+ :param server_url:
+ :param exp_no:
+ :return: message
+ """
+ if server_url.endswith('/') is False:
+ server_url = '%s/' % server_url
+ data_dir_url = '%sexp%d/Datafiles' % (server_url, exp_no)
+
+ does_exist, raw_lines = check_url(data_dir_url, read_lines=True)
+ if does_exist is False:
+ return "Experiment %d's URL %s cannot be found." % (exp_no, data_dir_url)
+
+ # Scan through the index page
+ scan_list = []
+ header = 'HB3A_exp%04d_scan' % exp_no
+ for line in raw_lines:
+ if line.count(header) > 0:
+ # try to find file HB3A_exp0123_scan6789.dat
+ term = line.split(header)[1].split('.dat')[0]
+ scan = int(term)
+ # check
+ if '%04d' % scan == term:
+ scan_list.append(scan)
+ # END_FOR
+ scan_list = sorted(scan_list)
+ if return_list is True:
+ return scan_list
+
+ message = 'Experiment %d: Scan from %d to %d' % (exp_no, scan_list[0], scan_list[-1])
+
+ return message
+
+
+def get_scans_list_local_disk(local_dir, exp_no):
+ """ Get scans from a specified directory on local disk
+ :param local_dir:
+ :param exp_no:
+ :return:
+ """
+ scan_list = []
+
+ file_names = os.listdir(local_dir)
+ header = 'HB3A_exp%04d_scan' % exp_no
+ for name in file_names:
+ if name.count(header) > 0:
+ scan = int(name.split(header)[1].split('.dat')[0])
+ scan_list.append(scan)
+
+ scan_list = sorted(scan_list)
+
+ if len(scan_list) == 0:
+ message = 'Experiment %d: No scan can be found.' % exp_no
+ else:
+ message = 'Experiment %d: Scan from %d to %d ' % (exp_no, scan_list[0], scan_list[-1])
+ num_skip_scans = scan_list[-1] - scan_list[0] + 1 - len(scan_list)
+ if num_skip_scans > 0:
+ message += 'with %d ' % num_skip_scans
+ else:
+ message += 'without '
+ message += 'missing scans.'
+
+ return message
+
+
+def parse_int_array(int_array_str):
+ """ Validate whether the string can be divided into integer strings.
+ Allowed: a, b, c-d, e, f
+ :param int_array_str:
+ :return:
+ """
+ int_array_str = str(int_array_str)
+ if int_array_str == "":
+ return True, []
+
+ # Split by ","
+ term_level_0 = int_array_str.split(",")
+ integer_list = []
+
+ # For each term
+ err_msg = ""
+ ret_status = True
+
+ for level0_term in term_level_0:
+ level0_term = level0_term.strip()
+
+ # split upon dash -
+ num_dashes = level0_term.count("-")
+ if num_dashes == 0:
+ # one integer
+ value_str = level0_term
+ try:
+ int_value = int(value_str)
+ if str(int_value) != value_str:
+ ret_status = False
+ err_msg = "Contains non-integer string %s." % value_str
+ except ValueError:
+ ret_status = False
+ err_msg = "String %s is not an integer." % (value_str)
+ else:
+ integer_list.append(int_value)
+
+ elif num_dashes == 1:
+ # Integer range
+ two_terms = level0_term.split("-")
+ temp_list = []
+ for i in xrange(2):
+ value_str = two_terms[i]
+ try:
+ int_value = int(value_str)
+ if str(int_value) != value_str:
+ ret_status = False
+ err_msg = "Contains non-integer string %s." % (value_str)
+ except ValueError:
+ ret_status = False
+ err_msg = "String %s is not an integer." % (value_str)
+ else:
+ temp_list.append(int_value)
+
+ # break loop
+ if ret_status is False:
+ break
+ # END_FOR(i)
+ integer_list.extend(range(temp_list[0], temp_list[1]+1))
+
+ else:
+ # Undefined situation
+ ret_status = False
+ err_msg = "Term %s contains more than 1 dash." % level0_term
+ # END-IF-ELSE
+
+ # break loop if something is wrong
+ if ret_status is False:
+ break
+ # END-FOR(level0_term)
+
+ # Return with false
+ if ret_status is False:
+ return False, err_msg
+
+ return True, integer_list
diff --git a/scripts/HFIR_4Circle_Reduction/guiutility.py b/scripts/HFIR_4Circle_Reduction/guiutility.py
new file mode 100644
index 0000000000000000000000000000000000000000..79237a5729470b372017478b24a0564159d67fb1
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/guiutility.py
@@ -0,0 +1,164 @@
+#
+# GUI Utility Methods
+#
+from PyQt4 import QtGui
+
+
+def parse_float_array(array_str):
+ """ Parse a string to an array of float
+ :param array_str:
+ :return: boolean, list of floats/error message
+ """
+ print array_str
+ assert isinstance(array_str, str)
+ array_str = array_str.replace(',', ' ')
+ array_str = array_str.replace('\n', ' ')
+ array_str = array_str.replace('\t ', ' ')
+ array_str = array_str.strip()
+ print '[DB] After processing: ', array_str
+
+ float_str_list = array_str.split()
+ float_list = list()
+ for float_str in float_str_list:
+ try:
+ value = float(float_str)
+ except ValueError as value_error:
+ return False, 'Unable to parse %s due to %s.' % (float_str, str(value_error))
+ else:
+ float_list.append(value)
+ # END-FOR
+
+ return True, float_list
+
+
+def parse_integer_list(array_str):
+ """ Parse a string to an array of integer separated by ','
+ also, the format as 'a-b' is supported too
+ :param array_str:
+ :return: boolean, list of floats/error message
+ """
+ assert isinstance(array_str, str)
+ array_str = array_str.replace(' ', '')
+ array_str = array_str.replace('\n', '')
+ array_str = array_str.replace('\t ', '')
+
+ int_str_list = array_str.split(',')
+ integer_list = list()
+ for int_str in int_str_list:
+
+ try:
+ int_value = int(int_str)
+ integer_list.append(int_value)
+ except ValueError:
+ num_dash = int_str.count('-')
+ if num_dash == 1:
+ terms = int_str.split('-')
+ try:
+ start_value = int(terms[0])
+ end_value = int(terms[1])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ elif num_dash == 2 and int_str.startswith('-'):
+ terms = int_str[1:].split('-')
+ try:
+ start_value = int(terms[0])*-1
+ end_value = int(terms[1])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ elif num_dash == 3:
+ terms = int_str.split('-')
+ try:
+ start_value = -1*int(terms[1])
+ end_value = -1*int(terms[3])
+ except ValueError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ except IndexError:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+ else:
+ raise RuntimeError('Unable to parse %s due to value error' % int_str)
+
+ integer_list.extend(xrange(start_value, end_value+1))
+ # END-FOR
+
+ return integer_list
+
+
+def parse_float_editors(line_edits):
+ """
+ :param line_edits:
+ :return: (True, list of floats); (False, error message)
+ """
+ # Set flag
+ return_single_value = False
+
+ if isinstance(line_edits, QtGui.QLineEdit) is True:
+ line_edit_list = [line_edits]
+ return_single_value = True
+ elif isinstance(line_edits, list) is True:
+ line_edit_list = line_edits
+ else:
+ raise RuntimeError('Input is not LineEdit or list of LineEdit.')
+
+ error_message = ''
+ float_list = []
+
+ for line_edit in line_edit_list:
+ assert isinstance(line_edit, QtGui.QLineEdit)
+ try:
+ str_value = str(line_edit.text()).strip()
+ float_value = float(str_value)
+ except ValueError as value_err:
+ error_message += 'Unable to parse to integer. %s\n' % (str(value_err))
+ else:
+ float_list.append(float_value)
+ # END-TRY
+ # END-FOR
+
+ if len(error_message) > 0:
+ return False, error_message
+ elif return_single_value is True:
+ return True, float_list[0]
+
+ return True, float_list
+
+
+def parse_integers_editors(line_edits):
+ """
+ :param line_edits:
+ :return: (True, list of integers); (False, error message)
+ """
+ # Set flag
+ return_single_value = False
+
+ if isinstance(line_edits, QtGui.QLineEdit) is True:
+ line_edit_list = [line_edits]
+ return_single_value = True
+ elif isinstance(line_edits, list) is True:
+ line_edit_list = line_edits
+ else:
+ raise RuntimeError('Input is not LineEdit or list of LineEdit.')
+
+ error_message = ''
+ integer_list = []
+
+ for line_edit in line_edit_list:
+ assert isinstance(line_edit, QtGui.QLineEdit)
+ try:
+ str_value = str(line_edit.text()).strip()
+ int_value = int(str_value)
+ except ValueError as value_err:
+ error_message += 'Unable to parse to integer. %s\n' % (str(value_err))
+ else:
+ if str_value != '%d' % int_value:
+ error_message += 'Value %s is not a proper integer.\n' % str_value
+ else:
+ integer_list.append(int_value)
+ # END-TRY
+ # END-FOR
+
+ if len(error_message) > 0:
+ return False, error_message
+ elif return_single_value is True:
+ return True, integer_list[0]
+
+ return True, integer_list
diff --git a/scripts/HFIR_4Circle_Reduction/hfctables.py b/scripts/HFIR_4Circle_Reduction/hfctables.py
new file mode 100644
index 0000000000000000000000000000000000000000..dba8cb64a3aefb4adff82b540655251d9fe41311
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/hfctables.py
@@ -0,0 +1,385 @@
+#pylint: disable=W0403,C0103,R0901,R0904
+import numpy
+import NTableWidget as tableBase
+
+# UB peak information table
+Peak_Integration_Table_Setup = [('Scan', 'int'),
+ ('Pt', 'int'),
+ ('H', 'float'),
+ ('K', 'float'),
+ ('L', 'float'),
+ ('Q_x', 'float'),
+ ('Q_y', 'float'),
+ ('Q_z', 'float'),
+ ('Intensity', 'float')]
+
+
+class IntegratePeaksTableWidget(tableBase.NTableWidget):
+ """
+ Extended table widget for peak integration
+ """
+ def __init__(self, parent):
+ """
+ :param parent:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(Peak_Integration_Table_Setup)
+
+ return
+
+
+class UBMatrixTable(tableBase.NTableWidget):
+ """
+ Extended table for UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ # Matrix
+ self._matrix = numpy.ndarray((3, 3), float)
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = 0.
+
+ return
+
+ def _set_to_table(self):
+ """
+ Set values in holder '_matrix' to TableWidget
+ :return:
+ """
+ for i_row in xrange(3):
+ for j_col in xrange(3):
+ self.update_cell_value(i_row, j_col, self._matrix[i_row][j_col])
+
+ return
+
+ def get_matrix(self):
+ """
+ Get the copy of the matrix
+ :return:
+ """
+ # print '[DB] MatrixTable: _Matrix = ', self._matrix
+ return self._matrix.copy()
+
+ def set_from_list(self, element_array):
+ """
+ Set table value including holder and QTable from a 1D numpy array
+ :param element_array:
+ :return:
+ """
+ # Check
+ assert isinstance(element_array, list)
+ assert len(element_array) == 9
+
+ # Set value
+ i_array = 0
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = element_array[i_array]
+ i_array += 1
+
+ # Set to table
+ self._set_to_table()
+
+ return
+
+ def set_from_matrix(self, matrix):
+ """
+ Set value to both holder and QTable from a numpy 3 x 3 matrix
+ :param matrix:
+ :return:
+ """
+ # Check
+ assert isinstance(matrix, numpy.ndarray)
+ assert matrix.shape == (3, 3)
+
+ for i in xrange(3):
+ for j in xrange(3):
+ self._matrix[i][j] = matrix[i][j]
+
+ self._set_to_table()
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ # self.init_size(3, 3)
+
+ for i in xrange(3):
+ for j in xrange(3):
+ self.set_value_cell(i, j)
+
+ self._set_to_table()
+
+ return
+
+
+# UB peak information table
+UB_Peak_Table_Setup = [('Scan', 'int'),
+ ('Pt', 'int'),
+ ('H', 'float'),
+ ('K', 'float'),
+ ('L', 'float'),
+ ('Q_x', 'float'),
+ ('Q_y', 'float'),
+ ('Q_z', 'float'),
+ ('Selected', 'checkbox'),
+ ('m1', 'float'),
+ ('Error', 'float')]
+
+
+class UBMatrixPeakTable(tableBase.NTableWidget):
+ """
+ Extended table for peaks used to calculate UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def get_exp_info(self, row_index):
+ """
+ Get experiment information from a row
+ :return: scan number, pt number
+ """
+ assert isinstance(row_index, int)
+
+ scan_number = self.get_cell_value(row_index, 0)
+ assert isinstance(scan_number, int)
+ pt_number = self.get_cell_value(row_index, 1)
+ assert isinstance(pt_number, int)
+
+ return scan_number, pt_number
+
+ def get_hkl(self, row_index):
+ """
+ Get reflection's miller index
+ :param row_index:
+ :return:
+ """
+ assert isinstance(row_index, int)
+
+ m_h = self.get_cell_value(row_index, 2)
+ m_k = self.get_cell_value(row_index, 3)
+ m_l = self.get_cell_value(row_index, 4)
+
+ assert isinstance(m_h, float)
+ assert isinstance(m_k, float)
+ assert isinstance(m_l, float)
+
+ return m_h, m_k, m_l
+
+ def get_scan_pt(self, row_number):
+ """
+ Get Scan and Pt from a row
+ :param row_number:
+ :return:
+ """
+ scan_number = self.get_cell_value(row_number, 0)
+ pt_number = self.get_cell_value(row_number, 1)
+
+ return scan_number, pt_number
+
+ def is_selected(self, row_index):
+ """
+
+ :return:
+ """
+ if row_index < 0 or row_index >= self.rowCount():
+ raise IndexError('Input row number %d is out of range [0, %d)' % (row_index, self.rowCount()))
+
+ col_index = UB_Peak_Table_Setup.index(('Selected', 'checkbox'))
+
+ return self.get_cell_value(row_index, col_index)
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(UB_Peak_Table_Setup)
+
+ return
+
+ def set_hkl(self, i_row, hkl, error=None):
+ """
+ Set HKL to table
+ :param irow:
+ :param hkl:
+ """
+ # Check
+ assert isinstance(i_row, int)
+ assert isinstance(hkl, list)
+
+ i_col_h = UB_Peak_Table_Setup.index(('H', 'float'))
+ i_col_k = UB_Peak_Table_Setup.index(('K', 'float'))
+ i_col_l = UB_Peak_Table_Setup.index(('L', 'float'))
+
+ self.update_cell_value(i_row, i_col_h, hkl[0])
+ self.update_cell_value(i_row, i_col_k, hkl[1])
+ self.update_cell_value(i_row, i_col_l, hkl[2])
+
+ if error is not None:
+ i_col_error = UB_Peak_Table_Setup.index(('Error', 'float'))
+ self.update_cell_value(i_row, i_col_error, error)
+
+ return
+
+ def update_hkl(self, i_row, h, k, l):
+ """ Update HKL value
+ """
+ self.update_cell_value(i_row, 2, h)
+ self.update_cell_value(i_row, 3, k)
+ self.update_cell_value(i_row, 4, l)
+
+ return
+
+
+# Processing status table
+Process_Table_Setup = [('Scan', 'int'),
+ ('Number Pt', 'int'),
+ ('Status', 'str'),
+ ('Merged Workspace', 'str'),
+ ('Group Name', 'str'),
+ ('Select', 'checkbox')]
+
+
+class ProcessTableWidget(tableBase.NTableWidget):
+ """
+ Extended table for peaks used to calculate UB matrix
+ """
+ def __init__(self, parent):
+ """
+
+ :param parent:
+ :return:
+ """
+ tableBase.NTableWidget.__init__(self, parent)
+
+ return
+
+ def append_scans(self, scans):
+ """ Append rows
+ :param scans:
+ :return:
+ """
+ # Check
+ assert isinstance(scans, list)
+
+ # Append rows
+ for scan in scans:
+ row_value_list = [scan, 0, 'In Queue', '', '', False]
+ status, err = self.append_row(row_value_list)
+ if status is False:
+ raise RuntimeError(err)
+
+ return
+
+ def setup(self):
+ """
+ Init setup
+ :return:
+ """
+ self.init_setup(Process_Table_Setup)
+
+ return
+
+ def set_scan_pt(self, scan_no, pt_list):
+ """
+ :param scan_no:
+ :param pt_list:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_no, int)
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_no == tmp_scan_no:
+ self.update_cell_value(i_row, 1, len(pt_list))
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_no
+
+ return ''
+
+ def set_status(self, scan_no, status):
+ """
+ Set the status for merging scan to QTable
+ :param status:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_no, int)
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_no == tmp_scan_no:
+ self.update_cell_value(i_row, 2, status)
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_no
+
+ return ''
+
+ def set_ws_names(self, scan_num, merged_md_name, ws_group_name):
+ """
+ Set the output workspace and workspace group's names to QTable
+ :param merged_md_name:
+ :param ws_group_name:
+ :return:
+ """
+ # Check
+ assert isinstance(scan_num, int)
+ assert isinstance(merged_md_name, str) or merged_md_name is None
+ assert isinstance(ws_group_name, str) or ws_group_name is None
+
+ num_rows = self.rowCount()
+ set_done = False
+ for i_row in xrange(num_rows):
+ tmp_scan_no = self.get_cell_value(i_row, 0)
+ if scan_num == tmp_scan_no:
+ if merged_md_name is not None:
+ self.update_cell_value(i_row, 3, merged_md_name)
+ if ws_group_name is not None:
+ self.update_cell_value(i_row, 4, ws_group_name)
+ set_done = True
+ break
+ # END-FOR
+
+ if set_done is False:
+ return 'Unable to find scan %d in table.' % scan_num
+
+ return
diff --git a/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
new file mode 100644
index 0000000000000000000000000000000000000000..152ffc29c4775c6f98b8b67befe0554a36d66032
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/mplgraphicsview.py
@@ -0,0 +1,1255 @@
+#pylint: disable=invalid-name,too-many-public-methods,too-many-arguments,non-parent-init-called,R0902,too-many-branches,C0302
+import os
+import numpy as np
+
+from PyQt4 import QtGui
+
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar2
+from matplotlib.figure import Figure
+import matplotlib.image
+
+MplLineStyles = ['-' , '--' , '-.' , ':' , 'None' , ' ' , '']
+MplLineMarkers = [
+ ". (point )",
+ "* (star )",
+ "x (x )",
+ "o (circle )",
+ "s (square )",
+ "D (diamond )",
+ ", (pixel )",
+ "v (triangle_down )",
+ "^ (triangle_up )",
+ "< (triangle_left )",
+ "> (triangle_right)",
+ "1 (tri_down )",
+ "2 (tri_up )",
+ "3 (tri_left )",
+ "4 (tri_right )",
+ "8 (octagon )",
+ "p (pentagon )",
+ "h (hexagon1 )",
+ "H (hexagon2 )",
+ "+ (plus )",
+ "d (thin_diamond )",
+ "| (vline )",
+ "_ (hline )",
+ "None (nothing )"]
+
+# Note: in colors, "white" is removed
+MplBasicColors = [
+ "black",
+ "red",
+ "blue",
+ "green",
+ "cyan",
+ "magenta",
+ "yellow"]
+
+
+class IndicatorManager(object):
+ """ Manager for all indicator lines
+ """
+ def __init__(self):
+ """
+
+ :return:
+ """
+ # Auto color index
+ self._colorIndex = 0
+ # Auto line ID
+ self._autoLineID = 1
+
+ self._lineManager = dict()
+ self._canvasLineKeyDict = dict()
+ self._indicatorTypeDict = dict() # value: 0 (horizontal), 1 (vertical), 2 (2-way)
+
+ return
+
+ def add_2way_indicator(self, x, x_min, x_max, y, y_min, y_max, color):
+ """
+
+ :param x:
+ :param x_min:
+ :param x_max:
+ :param y:
+ :param y_min:
+ :param y_max:
+ :param color:
+ :return:
+ """
+ # Set up indicator ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ # Set up vectors
+ vec_x_horizontal = np.array([x_min, x_max])
+ vec_y_horizontal = np.array([y, y])
+
+ vec_x_vertical = np.array([x, x])
+ vec_y_vertical = np.array([y_min, y_max])
+
+ #
+ self._lineManager[this_id] = [vec_x_horizontal, vec_y_horizontal, vec_x_vertical, vec_y_vertical, color]
+ self._indicatorTypeDict[this_id] = 2
+
+ return this_id
+
+ def add_horizontal_indicator(self, y, x_min, x_max, color):
+ """
+ Add a horizontal indicator
+ :param y:
+ :param x_min:
+ :param x_max:
+ :param color:
+ :return:
+ """
+ # Get ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ #
+ vec_x = np.array([x_min, x_max])
+ vec_y = np.array([y, y])
+
+ #
+ self._lineManager[this_id] = [vec_x, vec_y, color]
+ self._indicatorTypeDict[this_id] = 0
+
+ return this_id
+
+ def add_vertical_indicator(self, x, y_min, y_max, color):
+ """
+ Add a vertical indicator to data structure
+ :return: indicator ID
+ """
+ # Get ID
+ this_id = str(self._autoLineID)
+ self._autoLineID += 1
+
+ #
+ vec_x = np.array([x, x])
+ vec_y = np.array([y_min, y_max])
+
+ #
+ self._lineManager[this_id] = [vec_x, vec_y, color]
+ self._indicatorTypeDict[this_id] = 1
+
+ return this_id
+
+ def get_canvas_line_index(self, my_id):
+ """
+
+ :param my_id:
+ :return:
+ """
+ assert isinstance(my_id, str)
+
+ if my_id not in self._canvasLineKeyDict:
+ raise RuntimeError('Indicator ID %s cannot be found. Current keys are %s.' % (
+ my_id, str(sorted(self._canvasLineKeyDict.keys()))
+ ))
+ return self._canvasLineKeyDict[my_id]
+
+ def get_line_type(self, my_id):
+ """
+
+ :param my_id:
+ :return:
+ """
+ return self._indicatorTypeDict[my_id]
+
+ def get_2way_data(self, line_id):
+ """
+
+ :param line_id:
+ :return:
+ """
+ assert self._indicatorTypeDict.has_key(line_id)
+ assert self._indicatorTypeDict[line_id] == 2
+
+ vec_set = [self._lineManager[line_id][0:2], self._lineManager[line_id][2:4]]
+
+ return vec_set
+
+ def get_data(self, line_id):
+ """
+ Get line's vector x and vector y
+ :param line_id:
+ :return:
+ """
+ return self._lineManager[line_id][0], self._lineManager[line_id][1]
+
+ def get_line_style(self, line_id=None):
+ """
+
+ :param line_id:
+ :return:
+ """
+ assert isinstance(line_id, None)
+ return '--'
+
+ def get_live_indicator_ids(self):
+ """
+
+ :return:
+ """
+ return sorted(self._lineManager.keys())
+
+ def get_marker(self):
+ """
+ Get the marker a line
+ :param line_id:
+ :return:
+ """
+ return 'o'
+
+ def get_next_color(self):
+ """
+ Get next color by auto color index
+ :return: string as color
+ """
+ next_color = MplBasicColors[self._colorIndex]
+
+ # Advance and possibly reset color scheme
+ self._colorIndex += 1
+ if self._colorIndex == len(MplBasicColors):
+ self._colorIndex = 0
+
+ return next_color
+
+ def set_canvas_line_index(self, my_id, canvas_line_index):
+ """
+
+ :param my_id:
+ :param canvas_line_index:
+ :return:
+ """
+ self._canvasLineKeyDict[my_id] = canvas_line_index
+
+ def shift(self, my_id, dx, dy):
+ """
+
+ :param my_id:
+ :param dx:
+ :param dy:
+ :return:
+ """
+ print self._lineManager[my_id][0]
+
+ if self._indicatorTypeDict[my_id] == 0:
+ # horizontal
+ self._lineManager[my_id][1] += dy
+
+ elif self._indicatorTypeDict[my_id] == 1:
+ # vertical
+ self._lineManager[my_id][0] += dx
+
+ elif self._indicatorTypeDict[my_id] == 2:
+ # 2-way
+ self._lineManager[my_id][2] += dx
+ self._lineManager[my_id][1] += dy
+
+ else:
+ raise RuntimeError('Unsupported indicator of type %d' % self._indicatorTypeDict[my_id])
+
+ return
+
+ def update_indicators_range(self, x_range, y_range):
+ """
+ Update indicator's range
+ :param x_range:
+ :param y_range:
+ :return:
+ """
+ for i_id in self._lineManager.keys():
+ # NEXT - Need a new flag for direction of the indicating line, vertical or horizontal
+ if True:
+ self._lineManager[i_id][1][0] = y_range[0]
+ self._lineManager[i_id][1][-1] = y_range[1]
+ else:
+ self._lineManager[i_id][0][0] = x_range[0]
+ self._lineManager[i_id][0][-1] = x_range[1]
+
+ return
+
+
+class MplGraphicsView(QtGui.QWidget):
+ """ A combined graphics view including matplotlib canvas and
+ a navigation tool bar
+
+ Note: Merged with HFIR_Powder_Reduction.MplFigureCAnvas
+ """
+ def __init__(self, parent):
+ """ Initialization
+ """
+ # Initialize parent
+ QtGui.QWidget.__init__(self, parent)
+
+ # set up canvas
+ self._myCanvas = Qt4MplCanvas(self)
+ self._myToolBar = MyNavigationToolbar(self, self._myCanvas)
+
+ # set up layout
+ self._vBox = QtGui.QVBoxLayout(self)
+ self._vBox.addWidget(self._myCanvas)
+ self._vBox.addWidget(self._myToolBar)
+
+ # auto line's maker+color list
+ self._myLineMarkerColorList = []
+ self._myLineMarkerColorIndex = 0
+ self.setAutoLineMarkerColorCombo()
+
+ # Declaration of class variables
+ self._indicatorKey = None
+
+ # Indicator manager
+ self._myIndicatorsManager = IndicatorManager()
+
+ return
+
+ def add_line_set(self, vec_set, color, marker, line_style, line_width):
+ """ Add a set of line and manage together
+ :param vec_set:
+ :param color:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return:
+ """
+ key_list = list()
+ for vec_x, vec_y in vec_set:
+ temp_key = self._myCanvas.add_plot_1d(vec_x, vec_y, color=color, marker=marker,
+ line_style=line_style, line_width=line_width)
+ assert isinstance(temp_key, int)
+ assert temp_key >= 0
+ key_list.append(temp_key)
+
+ return key_list
+
+ def add_plot_1d(self, vec_x, vec_y, y_err=None, color=None, label="", x_label=None, y_label=None,
+ marker=None, line_style=None, line_width=1):
+ """ Add a new plot
+ """
+ line_key = self._myCanvas.add_plot_1d(vec_x, vec_y, y_err, color, label, x_label, y_label, marker, line_style,
+ line_width)
+
+ return line_key
+
+ def add_plot_1d_right(self, vec_x, vec_y, color=None, label='', marker=None, line_style=None, line_width=1):
+ """
+ Add 1 line (1-d plot) to right axis
+ :param vec_x:
+ :param vec_y:
+ :param color:
+ :param label:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return:
+ """
+ line_key = self._myCanvas.add_1d_plot_right(vec_x, vec_y, label=label,
+ color=color, marker=marker,
+ linestyle=line_style, linewidth=line_width)
+
+ return line_key
+
+ def add_2way_indicator(self, x=None, y=None, color=None, master_line=None):
+ """ Add a 2-way indicator following an existing line?
+ :param x:
+ :param y:
+ :param color:
+ :return:
+ """
+ if master_line is not None:
+ raise RuntimeError('Implement how to use master_line ASAP.')
+
+ x_min, x_max = self._myCanvas.getXLimit()
+ if x is None:
+ x = (x_min + x_max) * 0.5
+ else:
+ assert isinstance(x, float)
+
+ y_min, y_max = self._myCanvas.getYLimit()
+ if y is None:
+ y = (y_min + y_max) * 0.5
+ else:
+ assert isinstance(y, float)
+
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ my_id = self._myIndicatorsManager.add_2way_indicator(x, x_min, x_max,
+ y, y_min, y_max,
+ color)
+ vec_set = self._myIndicatorsManager.get_2way_data(my_id)
+
+ canvas_line_index = self.add_line_set(vec_set, color=color,
+ marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_horizontal_indicator(self, y=None, color=None):
+ """ Add an indicator line
+ """
+ # Default
+ if y is None:
+ y_min, y_max = self._myCanvas.getYLimit()
+ y = (y_min + y_max) * 0.5
+ else:
+ assert isinstance(y, float)
+
+ x_min, x_max = self._myCanvas.getXLimit()
+
+ # For color
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ # Form
+ my_id = self._myIndicatorsManager.add_horizontal_indicator(y, x_min, x_max, color)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(my_id)
+
+ canvas_line_index = self._myCanvas.add_plot_1d(vec_x=vec_x, vec_y=vec_y,
+ color=color, marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_vertical_indicator(self, x=None, color=None):
+ """
+ Add a vertical indicator line
+ :param x: None as the automatic mode using default from middle of canvas
+ :param color: None as the automatic mode using default
+ :return: indicator ID
+ """
+ # For indicator line's position
+ if x is None:
+ x_min, x_max = self._myCanvas.getXLimit()
+ x = (x_min + x_max) * 0.5
+ else:
+ assert isinstance(x, float)
+
+ y_min, y_max = self._myCanvas.getYLimit()
+
+ # For color
+ if color is None:
+ color = self._myIndicatorsManager.get_next_color()
+ else:
+ assert isinstance(color, str)
+
+ # Form
+ my_id = self._myIndicatorsManager.add_vertical_indicator(x, y_min, y_max, color)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(my_id)
+
+ canvas_line_index = self._myCanvas.add_plot_1d(vec_x=vec_x, vec_y=vec_y,
+ color=color, marker=self._myIndicatorsManager.get_marker(),
+ line_style=self._myIndicatorsManager.get_line_style(),
+ line_width=1)
+
+ self._myIndicatorsManager.set_canvas_line_index(my_id, canvas_line_index)
+
+ return my_id
+
+ def add_plot_2d(self, array2d, x_min, x_max, y_min, y_max, hold_prev_image=True, y_tick_label=None):
+ """
+ Add a 2D image to canvas
+ :param array2d: numpy 2D array
+ :param x_min:
+ :param x_max:
+ :param y_min:
+ :param y_max:
+ :param hold_prev_image:
+ :param y_tick_label:
+ :return:
+ """
+ self._myCanvas.addPlot2D(array2d, x_min, x_max, y_min, y_max, hold_prev_image, y_tick_label)
+
+ return
+
+
+ def addImage(self, imagefilename):
+ """ Add an image by file
+ """
+ # check
+ if os.path.exists(imagefilename) is False:
+ raise NotImplementedError("Image file %s does not exist." % (imagefilename))
+
+ self._myCanvas.addImage(imagefilename)
+
+ return
+
+ def clear_all_lines(self):
+ """
+ """
+ self._myCanvas.clear_all_1d_plots()
+
+ def clear_canvas(self):
+ """ Clear canvas
+ """
+ return self._myCanvas.clear_canvas()
+
+ def draw(self):
+ """ Draw to commit the change
+ """
+ return self._myCanvas.draw()
+
+ def evt_view_updated(self):
+ """ Event handling as canvas size updated
+ :return:
+ """
+ # update the indicator
+ new_x_range = self.getXLimit()
+ new_y_range = self.getYLimit()
+
+ self._myIndicatorsManager.update_indicators_range(new_x_range, new_y_range)
+ for indicator_key in self._myIndicatorsManager.get_live_indicator_ids():
+ canvas_line_id = self._myIndicatorsManager.get_canvas_line_index(indicator_key)
+ data_x, data_y = self._myIndicatorsManager.get_data(indicator_key)
+ self.updateLine(canvas_line_id, data_x, data_y)
+ # END-FOR
+
+ return
+
+ def getPlot(self):
+ """
+ """
+ return self._myCanvas.getPlot()
+
+ def getLastPlotIndexKey(self):
+ """ Get ...
+ """
+ return self._myCanvas.getLastPlotIndexKey()
+
+ def getXLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self._myCanvas.getXLimit()
+
+ def getYLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self._myCanvas.getYLimit()
+
+ def move_indicator(self, line_id, dx, dy):
+ """
+ Move the indicator line in horizontal
+ :param line_id:
+ :param dx:
+ :return:
+ """
+ # Shift value
+ self._myIndicatorsManager.shift(line_id, dx=dx, dy=dy)
+
+ # apply to plot on canvas
+ if self._myIndicatorsManager.get_line_type(line_id) < 2:
+ # horizontal or vertical
+ canvas_line_index = self._myIndicatorsManager.get_canvas_line_index(line_id)
+ vec_x, vec_y = self._myIndicatorsManager.get_data(line_id)
+ self._myCanvas.updateLine(ikey=canvas_line_index, vecx=vec_x, vecy=vec_y)
+ else:
+ # 2-way
+ canvas_line_index_h, canvas_line_index_v = self._myIndicatorsManager.get_canvas_line_index(line_id)
+ h_vec_set, v_vec_set = self._myIndicatorsManager.get_2way_data(line_id)
+
+ self._myCanvas.updateLine(ikey=canvas_line_index_h, vecx=h_vec_set[0], vecy=h_vec_set[1])
+ self._myCanvas.updateLine(ikey=canvas_line_index_v, vecx=v_vec_set[0], vecy=v_vec_set[1])
+
+ return
+
+ def remove_indicator(self, indicator_key):
+ """ Remove indicator line
+ :param indicator_key:
+ :return:
+ """
+ #
+ plot_id = self._myIndicatorsManager.get_canvas_line_index(indicator_key)
+ self._myCanvas.remove_plot_1d(plot_id)
+
+ return
+
+ def removePlot(self, ikey):
+ """
+ """
+ return self._myCanvas.remove_plot_1d(ikey)
+
+ def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
+ """
+ """
+ return self._myCanvas.updateLine(ikey, vecx, vecy, linestyle, linecolor, marker, markercolor)
+
+ def update_indicator(self, i_key, color):
+ """
+ Update indicator with new color
+ :param i_key:
+ :param vec_x:
+ :param vec_y:
+ :param color:
+ :return:
+ """
+ if self._myIndicatorsManager.get_line_type(i_key) < 2:
+ # horizontal or vertical
+ canvas_line_index = self._myIndicatorsManager.get_canvas_line_index(i_key)
+ self._myCanvas.updateLine(ikey=canvas_line_index, vecx=None, vecy=None, linecolor=color)
+ else:
+ # 2-way
+ canvas_line_index_h, canvas_line_index_v = self._myIndicatorsManager.get_canvas_line_index(i_key)
+ # h_vec_set, v_vec_set = self._myIndicatorsManager.get_2way_data(i_key)
+
+ self._myCanvas.updateLine(ikey=canvas_line_index_h, vecx=None, vecy=None, linecolor=color)
+ self._myCanvas.updateLine(ikey=canvas_line_index_v, vecx=None, vecy=None, linecolor=color)
+
+ return
+
+ def get_indicator_position(self, indicator_key):
+ """ Get position (x or y) of the indicator
+ :return:
+ """
+ # NEXT - Consider a better and more consistent return
+ vec_x, vec_y = self._myIndicatorsManager.get_data(indicator_key)
+ if vec_x[0] == vec_x[1]:
+ return vec_x[0]
+
+ return vec_y[0]
+
+ def getLineStyleList(self):
+ """
+ """
+ return MplLineStyles
+
+ def getLineMarkerList(self):
+ """
+ """
+ return MplLineMarkers
+
+ def getLineBasicColorList(self):
+ """
+ """
+ return MplBasicColors
+
+ def getDefaultColorMarkerComboList(self):
+ """ Get a list of line/marker color and marker style combination
+ as default to add more and more line to plot
+ """
+ return self._myCanvas.getDefaultColorMarkerComboList()
+
+ def getNextLineMarkerColorCombo(self):
+ """ As auto line's marker and color combo list is used,
+ get the NEXT marker/color combo
+ """
+ # get from list
+ marker, color = self._myLineMarkerColorList[self._myLineMarkerColorIndex]
+ # process marker if it has information
+ if marker.count(' (') > 0:
+ marker = marker.split(' (')[0]
+ print "[DB] Print line %d: marker = %s, color = %s" % (self._myLineMarkerColorIndex, marker, color)
+
+ # update the index
+ self._myLineMarkerColorIndex += 1
+ if self._myLineMarkerColorIndex == len(self._myLineMarkerColorList):
+ self._myLineMarkerColorIndex = 0
+
+ return marker, color
+
+ def resetLineColorStyle(self):
+ """ Reset the auto index for line's color and style
+ """
+ self._myLineMarkerColorIndex = 0
+ return
+
+ # NEXT-Urgent! - Find out difference between setXYLimit() and setXYLimits()
+ def setXYLimit(self, xmin, xmax, ymin, ymax):
+ """ Set X-Y limit automatically
+ """
+ self._myCanvas.axes.set_xlim([xmin, xmax])
+ self._myCanvas.axes.set_ylim([ymin, ymax])
+
+ self._myCanvas.draw()
+
+ return
+
+ def setXYLimits(self, xmin=None, xmax=None, ymin=None, ymax=None):
+ """
+ """
+ return self._myCanvas.setXYLimit(xmin, xmax, ymin, ymax)
+
+ def setAutoLineMarkerColorCombo(self):
+ """
+ """
+ self._myLineMarkerColorList = []
+ for marker in MplLineMarkers:
+ for color in MplBasicColors:
+ self._myLineMarkerColorList.append( (marker, color) )
+
+ return
+
+ def setLineMarkerColorIndex(self, newindex):
+ """
+ """
+ self._myLineMarkerColorIndex = newindex
+
+ return
+
+
+class Qt4MplCanvas(FigureCanvas):
+ """ A customized Qt widget for matplotlib figure.
+ It can be used to replace GraphicsView of QtGui
+ """
+ def __init__(self, parent):
+ """ Initialization
+ """
+ # from mpl_toolkits.axes_grid1 import host_subplot
+ # import mpl_toolkits.axisartist as AA
+ # import matplotlib.pyplot as plt
+
+ # Instantiating matplotlib Figure
+ self.fig = Figure()
+ self.fig.patch.set_facecolor('white')
+
+ if True:
+ self.axes = self.fig.add_subplot(111) # return: matplotlib.axes.AxesSubplot
+ self.axes2 = None
+ else:
+ self.axes = self.fig.add_host_subplot(111)
+
+ # Initialize parent class and set parent
+ FigureCanvas.__init__(self, self.fig)
+ self.setParent(parent)
+
+ # Set size policy to be able to expanding and resizable with frame
+ FigureCanvas.setSizePolicy(self, QtGui.QSizePolicy.Expanding,QtGui.QSizePolicy.Expanding)
+ FigureCanvas.updateGeometry(self)
+
+ # Variables to manage all lines/subplot
+ self._lineDict = {}
+ self._lineIndex = 0
+
+ # legend and color bar
+ self._colorBar = None
+
+ return
+
+ def add_plot_1d(self, vec_x, vec_y, y_err=None, color=None, label="", x_label=None, y_label=None,
+ marker=None, line_style=None, line_width=1):
+ """
+
+ :param vec_x: numpy array X
+ :param vec_y: numpy array Y
+ :param y_err:
+ :param color:
+ :param label:
+ :param x_label:
+ :param y_label:
+ :param marker:
+ :param line_style:
+ :param line_width:
+ :return: new key
+ """
+ # Check input
+ if isinstance(vec_x, np.ndarray) is False or isinstance(vec_y, np.ndarray) is False:
+ raise NotImplementedError('Input vec_x or vec_y for addPlot() must be numpy.array.')
+ plot_error = y_err is not None
+ if plot_error is True:
+ if isinstance(y_err, np.ndarray) is False:
+ raise NotImplementedError('Input y_err must be either None or numpy.array.')
+
+ if len(vec_x) != len(vec_y):
+ raise NotImplementedError('Input vec_x and vec_y must have same size.')
+ if plot_error is True and len(y_err) != len(vec_x):
+ raise NotImplementedError('Input vec_x, vec_y and y_error must have same size.')
+
+ # Hold previous data
+ self.axes.hold(True)
+
+ # process inputs and defaults
+ if color is None:
+ color = (0,1,0,1)
+ if marker is None:
+ marker = 'o'
+ if line_style is None:
+ line_style = '-'
+
+ # color must be RGBA (4-tuple)
+ if plot_error is False:
+ print "[DB] line_style = ", line_style, "line_width = ", line_width, "marker = ", marker, "color = ", color
+ r = self.axes.plot(vec_x, vec_y, color=color, marker=marker, linestyle=line_style,
+ label=label, linewidth=line_width)
+ # return: list of matplotlib.lines.Line2D object
+ else:
+ r = self.axes.errorbar(vec_x, vec_y, yerr=y_err, color=color, marker=marker, linestyle=line_style,
+ label=label, linewidth=line_width)
+
+ self.axes.set_aspect('auto')
+
+ # set x-axis and y-axis label
+ if x_label is not None:
+ self.axes.set_xlabel(x_label, fontsize=20)
+ if y_label is not None:
+ self.axes.set_ylabel(y_label, fontsize=20)
+
+ # set/update legend
+ self._setupLegend()
+
+ # Register
+ line_key = self._lineIndex
+ if len(r) == 1:
+ self._lineDict[line_key] = r[0]
+ self._lineIndex += 1
+ else:
+ print "Impoooooooooooooooosible! Return from plot is a %d-tuple. " % (len(r))
+
+ # Flush/commit
+ self.draw()
+
+ return line_key
+
+ def add_1d_plot_right(self, x, y, color=None, label="", x_label=None, ylabel=None, marker=None, linestyle=None,
+ linewidth=1):
+ """ Add a line (1-d plot) at right axis
+ """
+ if self.axes2 is None:
+ self.axes2 = self.axes.twinx()
+ # print self.par1, type(self.par1)
+
+ # Hold previous data
+ self.axes2.hold(True)
+
+ # Default
+ if color is None:
+ color = (0, 1, 0, 1)
+ if marker is None:
+ marker = 'o'
+ if linestyle is None:
+ linestyle = '-'
+
+ # Special default
+ if len(label) == 0:
+ label = 'right'
+ color = 'red'
+
+ # color must be RGBA (4-tuple)
+ r = self.axes2.plot(x, y, color=color, marker=marker, linestyle=linestyle,
+ label=label, linewidth=linewidth)
+ # return: list of matplotlib.lines.Line2D object
+
+ self.axes2.set_aspect('auto')
+
+ # set x-axis and y-axis label
+ if x_label is not None:
+ self.axes2.set_xlabel(x_label, fontsize=20)
+ if ylabel is not None:
+ self.axes2.set_ylabel(ylabel, fontsize=20)
+
+ # set/update legend
+ self._setupLegend()
+
+ # Register
+ line_key = -1
+ if len(r) == 1:
+ line_key = self._lineIndex
+ self._lineDict[line_key] = r[0]
+ self._lineIndex += 1
+ else:
+ print "Impoooooooooooooooosible!"
+
+ # Flush/commit
+ self.draw()
+
+ return line_key
+
+
+ def addPlot2D(self, array2d, xmin, xmax, ymin, ymax, holdprev, yticklabels=None):
+ """ Add a 2D plot
+
+ Arguments:
+ - yticklabels :: list of string for y ticks
+ """
+ # Release the current image
+ self.axes.hold(holdprev)
+
+ # Do plot
+ # y ticks will be shown on line 1, 4, 23, 24 and 30
+ # yticks = [1, 4, 23, 24, 30]
+ # self.axes.set_yticks(yticks)
+
+ # show image
+ imgplot = self.axes.imshow(array2d, extent=[xmin,xmax,ymin,ymax], interpolation='none')
+ # set y ticks as an option:
+ if yticklabels is not None:
+ # it will always label the first N ticks even image is zoomed in
+ print "--------> [FixMe]: Set up the Y-axis ticks is erroreous"
+ #self.axes.set_yticklabels(yticklabels)
+
+ # explicitly set aspect ratio of the image
+ self.axes.set_aspect('auto')
+
+ # Set color bar. plt.colorbar() does not work!
+ if self._colorBar is None:
+ # set color map type
+ imgplot.set_cmap('spectral')
+ self._colorBar = self.fig.colorbar(imgplot)
+ else:
+ self._colorBar.update_bruteforce(imgplot)
+
+ # Flush...
+ self._flush()
+
+ return
+
+ def addImage(self, imagefilename):
+ """ Add an image by file
+ """
+ #import matplotlib.image as mpimg
+
+ # set aspect to auto mode
+ self.axes.set_aspect('auto')
+
+ img = matplotlib.image.imread(str(imagefilename))
+ # lum_img = img[:,:,0]
+ # FUTURE : refactor for image size, interpolation and origin
+ imgplot = self.axes.imshow(img, extent=[0, 1000, 800, 0], interpolation='none', origin='lower')
+
+ # Set color bar. plt.colorbar() does not work!
+ if self._colorBar is None:
+ # set color map type
+ imgplot.set_cmap('spectral')
+ self._colorBar = self.fig.colorbar(imgplot)
+ else:
+ self._colorBar.update_bruteforce(imgplot)
+
+ self._flush()
+
+ return
+
+ def clear_all_1d_plots(self):
+ """ Remove all lines from the canvas
+ """
+ for ikey in self._lineDict.keys():
+ plot = self._lineDict[ikey]
+ if plot is None:
+ continue
+ if isinstance(plot, tuple) is False:
+ try:
+ self.axes.lines.remove(plot)
+ except ValueError as e:
+ print "[Error] Plot %s is not in axes.lines which has %d lines. Error mesage: %s" % (
+ str(plot), len(self.axes.lines), str(e))
+ self._lineDict[ikey] = None
+ else:
+ # error bar
+ plot[0].remove()
+ for line in plot[1]:
+ line.remove()
+ for line in plot[2]:
+ line.remove()
+ self._lineDict[ikey] = None
+ # ENDIF(plot)
+ # ENDFOR
+
+ self._setupLegend()
+
+ self.draw()
+
+ return
+
+ def clear_canvas(self):
+ """ Clear data including lines and image from canvas
+ """
+ # clear the image for next operation
+ self.axes.hold(False)
+
+ # Clear all lines
+ self.clear_all_1d_plots()
+
+ # clear image
+ self.axes.cla()
+ # Try to clear the color bar
+ if len(self.fig.axes) > 1:
+ self.fig.delaxes(self.fig.axes[1])
+ self._colorBar = None
+ # This clears the space claimed by color bar but destroys sub_plot too.
+ self.fig.clear()
+ # Re-create subplot
+ self.axes = self.fig.add_subplot(111)
+
+ # flush/commit
+ self._flush()
+
+ return
+
+
+ def getLastPlotIndexKey(self):
+ """ Get the index/key of the last added line
+ """
+ return self._lineIndex-1
+
+
+ def getPlot(self):
+ """ reture figure's axes to expose the matplotlib figure to PyQt client
+ """
+ return self.axes
+
+ def getXLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self.axes.get_xlim()
+
+ def getYLimit(self):
+ """ Get limit of Y-axis
+ """
+ return self.axes.get_ylim()
+
+ def setXYLimit(self, xmin, xmax, ymin, ymax):
+ """
+ """
+ # for X
+ xlims = self.axes.get_xlim()
+ xlims = list(xlims)
+ if xmin is not None:
+ xlims[0] = xmin
+ if xmax is not None:
+ xlims[1] = xmax
+ self.axes.set_xlim(xlims)
+
+ # for Y
+ ylims = self.axes.get_ylim()
+ ylims = list(ylims)
+ if ymin is not None:
+ ylims[0] = ymin
+ if ymax is not None:
+ ylims[1] = ymax
+ self.axes.set_ylim(ylims)
+
+ # try draw
+ self.draw()
+
+ return
+
+ def remove_plot_1d(self, plot_key):
+ """ Remove the line with its index as key
+ :param plot_key:
+ :return:
+ """
+ # self._lineDict[ikey].remove()
+ print 'Remove line... ',
+
+ # Get all lines in list
+ lines = self.axes.lines
+ assert isinstance(lines, list)
+
+ print 'Number of lines = %d, List: %s' % (len(lines), str(lines))
+ print 'Line to remove: key = %s, Line Dict has key = %s' % (str(plot_key), str(self._lineDict.has_key(plot_key)))
+
+ if plot_key in self._lineDict:
+ self.axes.lines.remove(self._lineDict[plot_key])
+ self._lineDict[plot_key] = None
+ else:
+ raise RuntimeError('Line with ID %s is not recorded.' % plot_key)
+
+ # Draw
+ self.draw()
+
+ return
+
+ def updateLine(self, ikey, vecx, vecy, linestyle=None, linecolor=None, marker=None, markercolor=None):
+ """
+ """
+ line = self._lineDict[ikey]
+
+ if vecx is not None and vecy is not None:
+ line.set_xdata(vecx)
+ line.set_ydata(vecy)
+
+ if linecolor is not None:
+ line.set_color(linecolor)
+
+ if linestyle is not None:
+ line.set_linestyle(linestyle)
+
+ if marker is not None:
+ line.set_marker(marker)
+
+ if markercolor is not None:
+ line.set_markerfacecolor(markercolor)
+
+ oldlabel = line.get_label()
+ line.set_label(oldlabel)
+
+ self.axes.legend()
+
+ # commit
+ self.draw()
+
+ return
+
+ def getLineStyleList(self):
+ """
+ """
+ return MplLineStyles
+
+
+ def getLineMarkerList(self):
+ """
+ """
+ return MplLineMarkers
+
+ def getLineBasicColorList(self):
+ """
+ """
+ return MplBasicColors
+
+ def getDefaultColorMarkerComboList(self):
+ """ Get a list of line/marker color and marker style combination
+ as default to add more and more line to plot
+ """
+ combolist = []
+ nummarkers = len(MplLineMarkers)
+ numcolors = len(MplBasicColors)
+
+ for i in xrange(nummarkers):
+ marker = MplLineMarkers[i]
+ for j in xrange(numcolors):
+ color = MplBasicColors[j]
+ combolist.append( (marker, color) )
+ # ENDFOR (j)
+ # ENDFOR(i)
+
+ return combolist
+
+ def _flush(self):
+ """ A dirty hack to flush the image
+ """
+ w, h = self.get_width_height()
+ self.resize(w+1,h)
+ self.resize(w,h)
+
+ return
+
+ def _setupLegend(self, location='best'):
+ """ Set up legend
+ self.axes.legend()
+ Handler is a Line2D object. Lable maps to the line object
+ """
+ loclist = [
+ "best",
+ "upper right",
+ "upper left",
+ "lower left",
+ "lower right",
+ "right",
+ "center left",
+ "center right",
+ "lower center",
+ "upper center",
+ "center"]
+
+ # Check legend location valid or not
+ if location not in loclist:
+ location = 'best'
+
+ handles, labels = self.axes.get_legend_handles_labels()
+ self.axes.legend(handles, labels, loc=location)
+ # print handles
+ # print labels
+ #self.axes.legend(self._myLegendHandlers, self._myLegentLabels)
+
+ return
+
+# END-OF-CLASS (MplGraphicsView)
+
+
+class MyNavigationToolbar(NavigationToolbar2):
+ """ A customized navigation tool bar attached to canvas
+ Note:
+ * home, left, right: will not disable zoom/pan mode
+ * zoom and pan: will turn on/off both's mode
+
+ Other methods
+ * drag_pan(self, event): event handling method for dragging canvas in pan-mode
+ """
+ NAVIGATION_MODE_NONE = 0
+ NAVIGATION_MODE_PAN = 1
+ NAVIGATION_MODE_ZOOM = 2
+
+ def __init__(self, parent, canvas):
+ """ Initialization
+ """
+ NavigationToolbar2.__init__(self, canvas, canvas)
+
+ self._myParent = parent
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+
+ return
+
+ def get_mode(self):
+ """
+ :return: integer as none/pan/zoom mode
+ """
+ return self._navigationMode
+
+ # Overriding base's methods
+ def draw(self):
+ """
+ Canvas is drawn called by pan(), zoom()
+ :return:
+ """
+ NavigationToolbar2.draw(self)
+
+ self._myParent.evt_view_updated()
+
+ return
+
+ def pan(self, *args):
+ """
+
+ :param args:
+ :return:
+ """
+ NavigationToolbar2.pan(self, args)
+
+ if self._navigationMode == MyNavigationToolbar.NAVIGATION_MODE_PAN:
+ # out of pan mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+ else:
+ # into pan mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_PAN
+
+ return
+
+ def zoom(self, *args):
+ """
+ Turn on/off zoom (zoom button)
+ :param args:
+ :return:
+ """
+ NavigationToolbar2.zoom(self, args)
+
+ if self._navigationMode == MyNavigationToolbar.NAVIGATION_MODE_ZOOM:
+ # out of zoom mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_NONE
+ else:
+ # into zoom mode
+ self._navigationMode = MyNavigationToolbar.NAVIGATION_MODE_ZOOM
+
+ return
+
+ def _update_view(self):
+ """
+ view update called by home(), back() and forward()
+ :return:
+ """
+ NavigationToolbar2._update_view(self)
+
+ self._myParent.evt_view_updated()
+
+ return
+
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
new file mode 100644
index 0000000000000000000000000000000000000000..bb11355d3c1b09e8e5b011cd8b698d64614939aa
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleControl.py
@@ -0,0 +1,1263 @@
+#pylint: disable=C0302,C0103,R0902,R0904,R0913,W0212,W0621,R0912
+################################################################################
+#
+# Controlling class
+#
+# == Data download and storage ==
+# - Local data storage (local-mode)
+# - Download from internet to cache (download-mode)
+#
+################################################################################
+import os
+import urllib2
+
+import numpy
+
+import mantid
+import mantid.simpleapi as api
+from mantid.api import AnalysisDataService
+
+DebugMode = True
+
+DET_X_SIZE = 256
+DET_Y_SIZE = 256
+
+
+class PeakInfo(object):
+ """ Class containing a peak's information for GUI
+ In order to manage some operations for a peak
+ It does not contain peak workspace but will hold
+ """
+ def __init__(self, parent):
+ """ Init
+ """
+ assert isinstance(parent, CWSCDReductionControl)
+
+ # Define class variable
+ self._myParent = parent
+ self._userHKL = [0, 0, 0]
+
+ self._myExpNumber = None
+ self._myScanNumber = None
+ self._myPtNumber = None
+
+ self._myPeakWSKey = (None, None, None)
+ self._myPeakIndex = None
+ # IPeak instance
+ self._myPeak = None
+
+ self._myLastPeakUB = None
+
+ return
+
+ def get_peak_workspace(self):
+ """
+ Get peak workspace related
+ :return:
+ """
+ assert isinstance(self._myPeakWSKey, tuple)
+ exp_number, scan_number, pt_number = self._myPeakWSKey
+
+ return self._myParent.get_ub_peak_ws(exp_number, scan_number, pt_number)[1]
+
+ def get_peak_ws_hkl(self):
+ """ Get HKL from PeakWorkspace
+ :return:
+ """
+ hkl = self._myPeak.getHKL()
+
+ return hkl.getX(), hkl.getY(), hkl.getZ()
+
+ def get_user_hkl(self):
+ """
+ Get HKL set to this object by client
+ :return: 3-tuple of float as (H, K, L)
+ """
+ hkl = self._userHKL
+
+ return hkl[0], hkl[1], hkl[2]
+
+ def set_from_run_info(self, exp_number, scan_number, pt_number):
+ """ Set from run information with parent
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ status, peak_ws = self._myParent.get_ub_peak_ws(exp_number, scan_number, pt_number)
+ if status is True:
+ self._myPeakWSKey = (exp_number, scan_number, pt_number)
+ self._myPeakIndex = 0
+ self._myPeak = peak_ws.getPeak(0)
+ else:
+ error_message = peak_ws
+ return False, error_message
+
+ self._myExpNumber = exp_number
+ self._myScanNumber = scan_number
+ self._myPtNumber = pt_number
+
+ return True, ''
+
+ def set_from_peak_ws(self, peak_ws, peak_index):
+ """
+ Set from peak workspace
+ :param peak_ws:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_ws, mantid.dataobjects.PeaksWorkspace)
+
+ # Get peak
+ try:
+ peak = peak_ws.getPeak(peak_index)
+ except RuntimeError as run_err:
+ raise RuntimeError(run_err)
+
+ self._myPeak = peak
+
+ return
+
+ def set_peak_ws_hkl_from_user(self):
+ """
+
+ :return:
+ """
+ # Check
+ if isinstance(self._myPeak, mantid.api.IPeak) is False:
+ raise RuntimeError('self._myPeakWS should be an instance of mantid.api.IPeak. '
+ 'But it is of instance of %s now.' % str(type(self._myPeak)))
+
+ # Get hkl
+ h, k, l = self._userHKL
+ print '[DB] PeakInfo Get User HKL = (%f, %f, %f) to IPeak ' % (h, k, l)
+
+ self._myPeak.setHKL(h, k, l)
+
+ return
+
+ def set_user_hkl(self, h, k, l):
+ """
+ Set HKL to this peak Info
+ :return:
+ """
+ assert isinstance(h, float)
+ assert isinstance(k, float)
+ assert isinstance(l, float)
+
+ self._userHKL[0] = h
+ self._userHKL[1] = k
+ self._userHKL[2] = l
+
+ print '[DB] PeakInfo Set User HKL to (%f, %f, %f) ' % (self._userHKL[0], self._userHKL[1], self._userHKL[2])
+
+ return
+
+ def getExpInfo(self):
+ """
+
+ :return: 3-tuple of integer as experiment number, scan number and Pt number
+ """
+ return self._myExpNumber, self._myScanNumber, self._myPtNumber
+
+ def getQSample(self):
+ """
+
+ :return: 3-tuple of floats as Qx, Qy, Qz
+ """
+ q_sample = self._myPeak.getQSampleFrame()
+ return q_sample.getX(), q_sample.getY(), q_sample.getZ()
+
+
+class CWSCDReductionControl(object):
+ """ Controlling class for reactor-based single crystal diffraction reduction
+ """
+ def __init__(self, instrument_name=None):
+ """ init
+ """
+ if isinstance(instrument_name, str):
+ self._instrumentName = instrument_name
+ elif instrument_name is None:
+ self._instrumentName = ''
+ else:
+ raise RuntimeError('Instrument name %s of type %s is not allowed.' % (str(instrument_name),
+ str(type(instrument_name))))
+
+ # Experiment number, data storage
+ # No Use/Confusing: self._expNumber = 0
+
+ self._dataDir = None
+ self._workDir = '/tmp'
+
+ self._myServerURL = ''
+
+ # Some set up
+ self._expNumber = None
+
+ # Container for MDEventWorkspace for each Pt.
+ self._myPtMDDict = dict()
+ # Container for loaded workspaces
+ self._mySpiceTableDict = {}
+ # Container for loaded raw pt workspace
+ self._myRawDataWSDict = dict()
+ # Container for PeakWorkspaces for calculating UB matrix
+ self._myUBPeakWSDict = dict()
+ # Container for UB matrix
+ self._myUBMatrixDict = dict()
+
+ # Peak Info
+ self._myPeakInfoDict = dict()
+ # Last UB matrix calculated
+ self._myLastPeakUB = None
+ # Flag for data storage
+ self._cacheDataOnly = False
+
+ # A dictionary to manage all loaded and processed MDEventWorkspaces
+ # self._expDataDict = {}
+
+ return
+
+ def add_peak_info(self, exp_number, scan_number, pt_number):
+ """ Add a peak info for calculating UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return: (boolean, PeakInfo/string)
+ """
+ has_peak_ws, peak_ws = self.get_ub_peak_ws(exp_number, scan_number, pt_number)
+ if has_peak_ws is False:
+ err_msg = 'No peak workspace found for Exp %s Scan %s Pt %s' % (
+ exp_number, scan_number, pt_number)
+ print '\n[DB] Fail to add peak info due to %s\n' % err_msg
+ return False, err_msg
+
+ if peak_ws.rowCount() > 1:
+ err_msg = 'There are more than 1 peak in PeaksWorkspace.'
+ print '\n[DB] Fail to add peak info due to %s\n' % err_msg
+ return False, err_msg
+
+ peak_info = PeakInfo(self)
+ peak_info.set_from_run_info(exp_number, scan_number, pt_number)
+
+ # Add to data management
+ self._myPeakInfoDict[(exp_number, scan_number, pt_number)] = peak_info
+
+ return True, peak_info
+
+ def calculate_ub_matrix(self, peak_info_list, a, b, c, alpha, beta, gamma):
+ """
+ Calculate UB matrix
+
+ Set Miller index from raw data in Workspace2D.
+ :param peakws:
+ :param a:
+ :param b:
+ :param c:
+ :param alpha:
+ :param beta:
+ :param gamma:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_info_list, list)
+ for peak_info in peak_info_list:
+ if isinstance(peak_info, PeakInfo) is False:
+ raise NotImplementedError('Input PeakList is of type %s.' % str(type(peak_info_list[0])))
+ assert isinstance(peak_info, PeakInfo)
+
+ if len(peak_info_list) < 2:
+ return False, 'Too few peaks are input to calculate UB matrix. Must be >= 2.'
+
+ # Construct a new peak workspace by combining all single peak
+ ub_peak_ws_name = 'Temp_UB_Peak'
+ ub_peak_ws = api.CloneWorkspace(InputWorkspace=peak_info_list[0].get_peak_workspace(),
+ OutputWorkspace=ub_peak_ws_name)
+
+ for i_peak_info in xrange(1, len(peak_info_list)):
+ # Set HKL as optional
+ peak_ws = peak_info_list[i_peak_info].get_peak_workspace()
+
+ # Combine peak workspace
+ ub_peak_ws = api.CombinePeaksWorkspaces(LHSWorkspace=ub_peak_ws,
+ RHSWorkspace=peak_ws,
+ CombineMatchingPeaks=False,
+ OutputWorkspace=ub_peak_ws_name)
+ # END-FOR(i_peak_info)
+
+ # Calculate UB matrix
+ try:
+ api.CalculateUMatrix(PeaksWorkspace=ub_peak_ws_name,
+ a=a, b=b, c=c, alpha=alpha, beta=beta, gamma=gamma)
+ except ValueError as val_err:
+ return False, str(val_err)
+
+ ub_matrix = ub_peak_ws.sample().getOrientedLattice().getUB()
+
+ self._myLastPeakUB = ub_peak_ws
+
+ return True, ub_matrix
+
+ def does_raw_loaded(self, exp_no, scan_no, pt_no):
+ """
+ Check whether the raw Workspace2D for a Pt. exists
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :return:
+ """
+ return (exp_no, scan_no, pt_no) in self._myRawDataWSDict
+
+ def does_spice_loaded(self, exp_no, scan_no):
+ """ Check whether a SPICE file has been loaded
+ :param exp_no:
+ :param scan_no:
+ :return:
+ """
+ return (exp_no, scan_no) in self._mySpiceTableDict
+
+ def download_spice_file(self, exp_number, scan_number, over_write):
+ """
+ Download a scan/pt data from internet
+ :param exp_number: experiment number
+ :param scan_number:
+ :return:
+ """
+ # Check
+ if exp_number is None:
+ exp_number = self._expNumber
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+
+ # Generate the URL for SPICE data file
+ file_url = '%sexp%d/Datafiles/HB3A_exp%04d_scan%04d.dat' % (self._myServerURL, exp_number,
+ exp_number, scan_number)
+ file_name = '%s_exp%04d_scan%04d.dat' % (self._instrumentName, exp_number, scan_number)
+ file_name = os.path.join(self._dataDir, file_name)
+ if os.path.exists(file_name) is True and over_write is False:
+ return True, file_name
+
+ # Download
+ try:
+ api.DownloadFile(Address=file_url, Filename=file_name)
+ except RuntimeError as run_err:
+ return False, str(run_err)
+
+ # Check file exist?
+ if os.path.exists(file_name) is False:
+ return False, "Unable to locate downloaded file %s." % file_name
+
+ return True, file_name
+
+ def download_spice_xml_file(self, scan_no, pt_no, exp_no=None, overwrite=False):
+ """ Download a SPICE XML file for one measurement in a scan
+ :param scan_no:
+ :param pt_no:
+ :param exp_no:
+ :param overwrite:
+ :return: tuple (boolean, local file name/error message)
+ """
+ # Experiment number
+ if exp_no is None:
+ exp_no = self._expNumber
+
+ # Form the target file name and path
+ xml_file_name = '%s_exp%d_scan%04d_%04d.xml' % (self._instrumentName, exp_no, scan_no, pt_no)
+ local_xml_file_name = os.path.join(self._dataDir, xml_file_name)
+ if os.path.exists(local_xml_file_name) is True and overwrite is False:
+ return True, local_xml_file_name
+
+ # Generate the URL for XML file
+ xml_file_url = '%sexp%d/Datafiles/%s' % (self._myServerURL, exp_no, xml_file_name)
+
+ # Download
+ try:
+ api.DownloadFile(Address=xml_file_url,
+ Filename=local_xml_file_name)
+ except RuntimeError as run_err:
+ return False, 'Unable to download Detector XML file %s dur to %s.' % (xml_file_name, str(run_err))
+
+ # Check file exist?
+ if os.path.exists(local_xml_file_name) is False:
+ return False, "Unable to locate downloaded file %s."%(local_xml_file_name)
+
+ return True, local_xml_file_name
+
+ def download_data_set(self, scan_list, overwrite=False):
+ """
+ Download data set including (1) spice file for a scan and (2) XML files for measurements
+ :param scan_list:
+ :return:
+ """
+ # Check
+ if self._expNumber is None:
+ raise RuntimeError('Experiment number is not set up for controller.')
+
+ error_message = ''
+
+ for scan_no in scan_list:
+ # Download single spice file for a run
+ status, ret_obj = self.download_spice_file(exp_number=self._expNumber,
+ scan_number=scan_no,
+ over_write=overwrite)
+
+ # Reject if SPICE file cannot download
+ if status is False:
+ error_message += '%s\n' % ret_obj
+ continue
+
+ # Load SPICE file to Mantid
+ spice_file_name = ret_obj
+ status, ret_obj = self.load_spice_scan_file(self._expNumber, scan_no, spice_file_name)
+ if status is False:
+ error_message = ret_obj
+ return False, error_message
+ else:
+ spice_table = self._mySpiceTableDict[(self._expNumber, scan_no)]
+ assert spice_table
+ pt_no_list = self._get_pt_list_from_spice_table(spice_table)
+
+ # Download all single-measurement file
+ for pt_no in pt_no_list:
+ status, ret_obj = self.download_spice_xml_file(scan_no, pt_no, overwrite=overwrite)
+ if status is False:
+ error_message += '%s\n' % ret_obj
+ # END-FOR
+ # END-FOR (scan_no)
+
+ return True, error_message
+
+ def existDataFile(self, scanno, ptno):
+ """
+ Check whether data file for a scan or pt number exists
+ :param scanno:
+ :param ptno:
+ :return:
+ """
+ # Check spice file
+ spice_file_name = '%s_exp%04d_scan%04d.dat'%(self._instrumentName,
+ self._expNumber, scanno)
+ spice_file_name = os.path.join(self._dataDir, spice_file_name)
+ if os.path.exists(spice_file_name) is False:
+ return False, 'Spice data file %s cannot be found.'% spice_file_name
+
+ # Check xml file
+ xmlfilename = '%s_exp%d_scan%04d_%04d.xml'%(self._instrumentName, self._expNumber,
+ scanno, ptno)
+ xmlfilename = os.path.join(self._dataDir, xmlfilename)
+ if os.path.exists(xmlfilename) is False:
+ return (False, "Pt. XML file %s cannot be found."%(xmlfilename))
+
+ return True, ""
+
+ def find_peak(self, exp_number, scan_number, pt_number):
+ """ Find 1 peak in sample Q space for UB matrix
+ :param scan_number:
+ :param pt_number:
+ :return:tuple as (boolean, object) such as (false, error message) and (true, PeakInfo object)
+
+ This part will be redo as 11847_Load_HB3A_Experiment
+ """
+ # Check
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Download or make sure data are there
+ status_sp, err_msg_sp = self.download_spice_file(exp_number, scan_number, over_write=False)
+ status_det, err_msg_det = self.download_spice_xml_file(scan_number, pt_number, exp_number,
+ overwrite=False)
+ if status_sp is False or status_det is False:
+ return False, 'Unable to access data (1) %s (2) %s' % (err_msg_sp, err_msg_det)
+
+ # Collect reduction information: example
+ exp_info_ws_name = get_pt_info_ws_name(exp_number, scan_number)
+ virtual_instrument_info_table_name = get_virtual_instrument_table_name(exp_number, scan_number, pt_number)
+ api.CollectHB3AExperimentInfo(
+ ExperimentNumber=exp_number,
+ GenerateVirtualInstrument=False,
+ ScanList=[scan_number],
+ PtLists=[-1, pt_number],
+ DataDirectory=self._dataDir,
+ GetFileFromServer=False,
+ Detector2ThetaTolerance=0.01,
+ OutputWorkspace=exp_info_ws_name,
+ DetectorTableWorkspace=virtual_instrument_info_table_name)
+
+ # Load XML file to MD
+ pt_md_ws_name = get_single_pt_md_name(exp_number, scan_number, pt_number)
+ api.ConvertCWSDExpToMomentum(InputWorkspace=exp_info_ws_name,
+ CreateVirtualInstrument=False,
+ OutputWorkspace=pt_md_ws_name,
+ Directory=self._dataDir)
+
+ # Find peak in Q-space
+ pt_peak_ws_name = get_single_pt_peak_ws_name(exp_number, scan_number, pt_number)
+ api.FindPeaksMD(InputWorkspace=pt_md_ws_name, MaxPeaks=10,
+ DensityThresholdFactor=0.01, OutputWorkspace=pt_peak_ws_name)
+ peak_ws = AnalysisDataService.retrieve(pt_peak_ws_name)
+ pt_md_ws = AnalysisDataService.retrieve(pt_md_ws_name)
+ self._myPtMDDict[(exp_number, scan_number, pt_number)] = pt_md_ws
+
+ num_peaks = peak_ws.getNumberPeaks()
+ if num_peaks != 1:
+ err_msg = 'Find %d peak from scan %d pt %d. ' \
+ 'For UB matrix calculation, 1 and only 1 peak is allowed' % (num_peaks, scan_number, pt_number)
+ return False, err_msg
+ else:
+ self._add_ub_peak_ws(exp_number, scan_number, pt_number, peak_ws)
+ status, ret_obj = self.add_peak_info(exp_number, scan_number, pt_number)
+ if status is True:
+ pass
+ # peak_info = ret_obj
+ # peak_info.set_md_ws(pt_md_ws)
+ else:
+ err_msg = ret_obj
+ return False, err_msg
+
+ return True, ''
+
+ def get_experiment(self):
+ """
+ Get experiment number
+ :return:
+ """
+ return self._expNumber
+
+ def get_pt_numbers(self, exp_no, scan_no, load_spice_scan=False):
+ """ Get Pt numbers (as a list) for a scan in an experiment
+ :param exp_no:
+ :param scan_no:
+ :param load_spice_scan:
+ :return: (Boolean, Object) as (status, pt number list/error message)
+ """
+ # Check
+ if exp_no is None:
+ exp_no = self._expNumber
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+
+ # Get workspace
+ table_ws = self._get_spice_workspace(exp_no, scan_no)
+ if table_ws is None:
+ if load_spice_scan is False:
+ return False, 'Spice file for Exp %d Scan %d is not loaded.' % (exp_no, scan_no)
+ else:
+ status, error_message = self.load_spice_scan_file(exp_no, scan_no)
+ if status is True:
+ table_ws = self._get_spice_workspace(exp_no, scan_no)
+ if table_ws is None:
+ raise NotImplementedError('Logic error! Cannot happen!')
+ else:
+ return False, 'Unable to load Spice file for Exp %d Scan %d due to %s.' % (
+ exp_no, scan_no, error_message)
+
+ col_name_list = table_ws.getColumnNames()
+ i_pt = col_name_list.index('Pt.')
+ if i_pt < 0 or i_pt >= len(col_name_list):
+ return False, 'No column with name Pt. can be found in SPICE table.'
+
+ pt_number_list = []
+ num_rows = table_ws.rowCount()
+ for i in xrange(num_rows):
+ pt_number = table_ws.cell(i, i_pt)
+ pt_number_list.append(pt_number)
+
+ return True, pt_number_list
+
+ def get_raw_detector_counts(self, exp_no, scan_no, pt_no):
+ """
+ Get counts on raw detector
+ :param scan_no:
+ :param pt_no:
+ :return: boolean, 2D numpy data
+ """
+ # Get workspace (in memory or loading)
+ raw_ws = self.get_raw_data_workspace(exp_no, scan_no, pt_no)
+ if raw_ws is None:
+ return False, 'Raw data for Exp %d Scan %d Pt %d is not loaded.' % (exp_no, scan_no, pt_no)
+
+ # Convert to numpy array
+ array2d = numpy.ndarray(shape=(DET_X_SIZE, DET_Y_SIZE), dtype='float')
+ for i in xrange(DET_X_SIZE):
+ for j in xrange(DET_Y_SIZE):
+ array2d[i][j] = raw_ws.readY(i * DET_X_SIZE + j)[0]
+
+ return array2d
+
+ def get_sample_log_value(self, exp_number, scan_number, pt_number, log_name):
+ """
+ Get sample log's value
+ :param exp_number:
+ :param scan_number:167
+ :param pt_number:
+ :param log_name:
+ :return: float
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+ assert isinstance(log_name, str)
+ try:
+ md_ws = self._myPtMDDict[(exp_number, scan_number, pt_number)]
+ except KeyError as ke:
+ return 'Unable to find log value %s due to %s.' % (log_name, str(ke))
+
+ return md_ws.getExperimentInfo(0).run().getProperty(log_name).value
+
+ def get_peak_info(self, exp_number, scan_number, pt_number):
+ """
+ get peak information instance
+ :param exp_number: experiment number. if it is None, then use the current exp number
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ # Check for type
+ if exp_number is None:
+ exp_number = self._expNumber
+
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Check for existence
+ if (exp_number, scan_number, pt_number) not in self._myUBPeakWSDict: # self._myPeakInfoDict:
+ err_msg = 'Unable to find PeakInfo for Exp %d Scan %d Pt %d. ' \
+ 'Existing keys are %s' % (exp_number, scan_number, pt_number,
+ str(self._myUBPeakWSDict.keys()))
+ return False, err_msg
+
+ print '[DB] PeakInfoDictionary Keys = %s' % str(self._myPeakInfoDict.keys())
+
+ return True, self._myPeakInfoDict[(exp_number, scan_number, pt_number)]
+
+ def get_ub_peak_ws(self, exp_number, scan_number, pt_number):
+ """
+ Get peak workspace for the peak picked to calculate UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ if (exp_number, scan_number, pt_number) not in self._myUBPeakWSDict:
+ return False, 'Exp %d Scan %d Pt %d has no peak workspace.' % (exp_number,
+ scan_number,
+ pt_number)
+
+ return True, self._myUBPeakWSDict[(exp_number, scan_number, pt_number)]
+
+ def index_peak(self, ub_matrix, scan_number, pt_number):
+ """ Index peaks in a Pt.
+ :param ub_matrix: numpy.ndarray (3, 3)
+ :param scan_number:
+ :param pt_number:
+ :return: boolean, object (list of HKL or error message)
+ """
+ # Check
+ assert isinstance(ub_matrix, numpy.ndarray)
+ assert ub_matrix.shape == (3, 3)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Find out the peak workspace
+ exp_num = self._expNumber
+ if (exp_num, scan_number, pt_number) in self._myUBPeakWSDict is False:
+ err_msg = 'No PeakWorkspace is found for exp %d scan %d pt %d' % (
+ exp_num, scan_number, pt_number)
+ return False, err_msg
+
+ peak_ws = self._myUBPeakWSDict[(exp_num, scan_number, pt_number)]
+ ub_1d = ub_matrix.reshape(9,)
+ print '[DB] UB matrix = ', ub_1d
+
+ # Set UB
+ api.SetUB(Workspace=peak_ws, UB=ub_1d)
+
+ # Note: IndexPeaks and CalcualtePeaksHKL do the same job
+ # while IndexPeaks has more control on the output
+ num_peak_index, error = api.IndexPeaks(PeaksWorkspace=peak_ws,
+ Tolerance=0.4,
+ RoundHKLs=False)
+
+ if num_peak_index == 0:
+ return False, 'No peak can be indexed.'
+ elif num_peak_index > 1:
+ raise RuntimeError('Case for PeaksWorkspace containing more than 1 peak is not '
+ 'considered. Contact developer for this issue.')
+ else:
+ hkl_v3d = peak_ws.getPeak(0).getHKL()
+ hkl = [hkl_v3d.X(), hkl_v3d.Y(), hkl_v3d.Z()]
+
+ return True, (hkl, error)
+
+ def load_spice_scan_file(self, exp_no, scan_no, spice_file_name=None):
+ """
+ Load a SPICE scan file to table workspace and run information matrix workspace.
+ :param scan_no:
+ :param spice_file_name:
+ :return: status (boolean), error message (string)
+ """
+ # Default for exp_no
+ if exp_no is None:
+ exp_no = self._expNumber
+
+ # Check whether the workspace has been loaded
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ out_ws_name = get_spice_table_name(exp_no, scan_no)
+ if (exp_no, scan_no) in self._mySpiceTableDict:
+ return True, out_ws_name
+
+ # Form standard name for a SPICE file if name is not given
+ if spice_file_name is None:
+ spice_file_name = os.path.join(self._dataDir, get_spice_file_name(exp_no, scan_no))
+
+ # Download SPICE file if necessary
+ if os.path.exists(spice_file_name) is False:
+ self.download_spice_file(exp_no, scan_no, over_write=True)
+
+ try:
+ spice_table_ws, info_matrix_ws = api.LoadSpiceAscii(Filename=spice_file_name,
+ OutputWorkspace=out_ws_name,
+ RunInfoWorkspace='TempInfo')
+ api.DeleteWorkspace(Workspace=info_matrix_ws)
+ except RuntimeError as run_err:
+ return False, 'Unable to load SPICE data %s due to %s' % (spice_file_name, str(run_err))
+
+ # Store
+ self._add_spice_workspace(exp_no, scan_no, spice_table_ws)
+
+ return True, out_ws_name
+
+ def load_spice_xml_file(self, exp_no, scan_no, pt_no, xml_file_name=None):
+ """
+ Load SPICE's XML file to
+ :param scan_no:
+ :param pt_no:
+ :return:
+ """
+ # Form XMIL file as ~/../HB3A_exp355_scan%04d_%04d.xml'%(scan_no, pt)
+ if xml_file_name is None:
+ xml_file_name = os.path.join(self._dataDir,
+ 'HB3A_exp%d_scan%04d_%04d.xml' % (exp_no, scan_no, pt_no))
+
+ # Get spice table
+ spice_table_ws = self._get_spice_workspace(exp_no, scan_no)
+ assert isinstance(spice_table_ws, mantid.dataobjects.TableWorkspace)
+ spice_table_name = spice_table_ws.name()
+
+ # Load SPICE Pt. file
+ # spice_table_name = 'Table_Exp%d_Scan%04d' % (exp_no, scan_no)
+ pt_ws_name = get_raw_data_workspace_name(exp_no, scan_no, pt_no)
+ try:
+ ret_obj = api.LoadSpiceXML2DDet(Filename=xml_file_name,
+ OutputWorkspace=pt_ws_name,
+ DetectorGeometry='256,256',
+ SpiceTableWorkspace=spice_table_name,
+ PtNumber=pt_no)
+ except RuntimeError as run_err:
+ return False, str(run_err)
+
+ pt_ws = ret_obj
+
+ # Add data storage
+ self._add_raw_workspace(exp_no, scan_no, pt_no, pt_ws)
+
+ return True, pt_ws_name
+
+ def group_workspaces(self, exp_number, group_name):
+ """
+
+ :return:
+ """
+ # Find out the input workspace name
+ ws_names_str = ''
+ for key in self._myRawDataWSDict.keys():
+ if key[0] == exp_number:
+ ws_names_str += '%s,' % self._myRawDataWSDict[key].name()
+
+ for key in self._mySpiceTableDict.keys():
+ if key[0] == exp_number:
+ ws_names_str += '%s,' % self._mySpiceTableDict[key].name()
+
+ # Check
+ if len(ws_names_str) == 0:
+ return False, 'No workspace is found for experiment %d.' % exp_number
+
+ # Remove last ','
+ ws_names_str = ws_names_str[:-1]
+
+ # Group
+ api.GroupWorkspaces(InputWorkspaces=ws_names_str,
+ OutputWorkspace=group_name)
+
+ return
+
+ def merge_pts_in_scan(self, exp_no, scan_no, target_ws_name, target_frame):
+ """
+ Merge Pts in Scan
+ All the workspaces generated as internal results will be grouped
+ :param exp_no:
+ :param scan_no:
+ :param target_ws_name:
+ :param target_frame:
+ :return: (merged workspace name, workspace group name)
+ """
+ # Check
+ if exp_no is None:
+ exp_no = self._expNumber
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(target_frame, str)
+ assert isinstance(target_ws_name, str)
+
+ ub_matrix_1d = None
+
+ # Target frame
+ if target_frame.lower().startswith('hkl'):
+ target_frame = 'hkl'
+ ub_matrix_1d = self._myUBMatrixDict[self._expNumber].reshape(9,)
+ elif target_frame.lower().startswith('q-sample'):
+ target_frame = 'qsample'
+
+ else:
+ raise RuntimeError('Target frame %s is not supported.' % target_frame)
+
+ # Process data and save
+ status, pt_num_list = self.get_pt_numbers(exp_no, scan_no, True)
+ if status is False:
+ err_msg = pt_num_list
+ return False, err_msg
+ else:
+ print '[DB] Number of Pts for Scan %d is %d' % (scan_no, len(pt_num_list))
+ print '[DB] Data directory: %s' % self._dataDir
+ max_pts = 0
+ ws_names_str = ''
+ ws_names_to_group = ''
+
+ for pt in pt_num_list:
+ try:
+ self.download_spice_xml_file(scan_no, pt, overwrite=False)
+ api.CollectHB3AExperimentInfo(ExperimentNumber=exp_no, ScanList='%d' % scan_no, PtLists='-1,%d' % pt,
+ DataDirectory=self._dataDir,
+ GenerateVirtualInstrument=False,
+ OutputWorkspace='ScanPtInfo_Exp%d_Scan%d' % (exp_no, scan_no),
+ DetectorTableWorkspace='MockDetTable')
+
+ out_q_name = 'HB3A_Exp%d_Scan%d_Pt%d_MD' % (exp_no, scan_no, pt)
+ api.ConvertCWSDExpToMomentum(InputWorkspace='ScanPtInfo_Exp406_Scan%d' % scan_no,
+ CreateVirtualInstrument=False,
+ OutputWorkspace=out_q_name,
+ Directory=self._dataDir)
+
+ ws_names_to_group += out_q_name + ','
+ if target_frame == 'hkl':
+ out_hkl_name = 'HKL_Scan%d_Pt%d' % (scan_no, pt)
+ api.ConvertCWSDMDtoHKL(InputWorkspace=out_q_name,
+ UBMatrix=ub_matrix_1d,
+ OutputWorkspace=out_hkl_name)
+ ws_names_str += out_hkl_name + ','
+ ws_names_to_group += out_hkl_name + ','
+ else:
+ ws_names_str += out_q_name + ','
+
+ except RuntimeError as e:
+ print '[Error] Reducing scan %d pt %d due to %s' % (scan_no, pt, str(e))
+ continue
+
+ else:
+ max_pts = pt
+ # END-FOR
+
+ # Merge
+ if target_frame == 'qsample':
+ out_ws_name = target_ws_name + '_QSample'
+ elif target_frame == 'hkl':
+ out_ws_name = target_ws_name + '_HKL'
+ else:
+ raise RuntimeError('Impossible to have target frame %s' % target_frame)
+
+ ws_names_str = ws_names_str[:-1]
+ api.MergeMD(InputWorkspaces=ws_names_str, OutputWorkspace=out_ws_name, SplitInto=max_pts)
+
+ # Group workspaces
+ group_name = 'Group_Exp406_Scan%d' % scan_no
+ api.GroupWorkspaces(InputWorkspaces=ws_names_to_group, OutputWorkspace=group_name)
+ spice_table_name = get_spice_table_name(exp_no, scan_no)
+ api.GroupWorkspaces(InputWorkspaces='%s,%s' % (group_name, spice_table_name), OutputWorkspace=group_name)
+
+ ret_tup = out_ws_name, group_name
+
+ return ret_tup
+
+ def set_server_url(self, server_url):
+ """
+ Set URL for server to download the data
+ :param server_url:
+ :return:
+ """
+ # Server URL must end with '/'
+ self._myServerURL = str(server_url)
+ if self._myServerURL.endswith('/') is False:
+ self._myServerURL += '/'
+
+ # Test URL valid or not
+ is_url_good = False
+ error_message = None
+ try:
+ result = urllib2.urlopen(self._myServerURL)
+ except urllib2.HTTPError, err:
+ error_message = str(err.code)
+ except urllib2.URLError, err:
+ error_message = str(err.args)
+ else:
+ is_url_good = True
+ result.close()
+
+ if error_message is None:
+ error_message = ''
+ else:
+ error_message = 'Unable to open data server URL: %s due to %s.' % (server_url, error_message)
+
+ return is_url_good, error_message
+
+ def setWebAccessMode(self, mode):
+ """
+ Set data access mode form server
+ :param mode:
+ :return:
+ """
+ if isinstance(mode, str) is False:
+ raise RuntimeError('Input mode is not string')
+
+ if mode == 'cache':
+ self._cacheDataOnly = True
+ elif mode == 'download':
+ self._cacheDataOnly = False
+
+ return
+
+ def set_local_data_dir(self, local_dir):
+ """
+ Set local data storage
+ :param local_dir:
+ :return:
+ """
+ # Get absolute path
+ if os.path.isabs(local_dir) is False:
+ # Input is relative path to current working directory
+ cwd = os.getcwd()
+ local_dir = os.path.join(cwd, local_dir)
+
+ # Create cache directory if necessary
+ if os.path.exists(local_dir) is False:
+ try:
+ os.mkdir(local_dir)
+ except OSError as os_err:
+ return False, str(os_err)
+
+ # Check whether the target is writable
+ if os.access(local_dir, os.W_OK) is False:
+ return False, 'Specified local data directory %s is not writable.' % local_dir
+
+ # Successful
+ self._dataDir = local_dir
+
+ return True, ''
+
+ def set_ub_matrix(self, exp_number, ub_matrix):
+ """
+ Set up UB matrix to _UBMatrix dictionary
+ :param exp_number:
+ :param ub_matrix:
+ :return:
+ """
+ # Check
+ if exp_number is None:
+ exp_number = self._expNumber
+
+ assert isinstance(exp_number, int)
+ assert isinstance(ub_matrix, numpy.ndarray)
+ assert ub_matrix.shape == (3, 3)
+
+ # Set up
+ self._myUBMatrixDict[exp_number] = ub_matrix
+
+ def set_working_directory(self, work_dir):
+ """
+ Set up the directory for working result
+ :return: (boolean, string)
+ """
+ if os.path.exists(work_dir) is False:
+ try:
+ os.mkdir(work_dir)
+ except OSError as os_err:
+ return False, 'Unable to create working directory %s due to %s.' % (work_dir, str(os_err))
+ elif os.access(work_dir, os.W_OK) is False:
+ return False, 'User specified working directory %s is not writable.' % work_dir
+
+ self._workDir = work_dir
+
+ return True, ''
+
+ def set_instrument_name(self, instrument_name):
+ """
+ Set instrument name
+ :param instrument_name:
+ :return:
+ """
+ # Check
+ if isinstance(instrument_name, str) is False:
+ return False, 'Input instrument name is not a string but of type %s.' % str(type(instrument_name))
+ if len(instrument_name) == 0:
+ return False, 'Input instrument name is an empty string.'
+
+ self._instrumentName = instrument_name
+
+ return True, ''
+
+ def set_exp_number(self, exp_number):
+ """ Add experiment number
+ :param exp_number:
+ :return:
+ """
+ assert isinstance(exp_number, int)
+ self._expNumber = exp_number
+
+ return True
+
+ def set_hkl_to_peak(self, exp_number, scan_number, pt_number):
+ """
+ Get HKL as _h, _k, _l from MDEventWorkspace. It is for HB3A only
+ :return:
+ """
+ status, peak_info = self.get_peak_info(exp_number, scan_number, pt_number)
+ if status is False:
+ err_msg = peak_info
+ return False, err_msg
+
+ md_ws = self._myPtMDDict[(exp_number, scan_number, pt_number)]
+ assert md_ws.getNumExperimentInfo() == 1
+ exp_info = md_ws.getExperimentInfo(0)
+
+ try:
+ m_h = float(exp_info.run().getProperty('_h').value)
+ m_k = float(exp_info.run().getProperty('_k').value)
+ m_l = float(exp_info.run().getProperty('_l').value)
+ except RuntimeError as error:
+ return False, 'Unable to retrieve HKL due to %s.' % (str(error))
+
+ peak_ws = peak_info.get_peak_workspace()
+ peak = peak_ws.getPeak(0)
+ peak.setHKL(m_h, m_k, m_l)
+
+ return True, (m_h, m_k, m_l)
+
+ def _add_raw_workspace(self, exp_no, scan_no, pt_no, raw_ws):
+ """ Add raw Pt.'s workspace
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :param raw_ws: workspace or name of the workspace
+ :return: None
+ """
+ # Check
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(pt_no, int)
+
+ if isinstance(raw_ws, str):
+ # Given by name
+ matrix_ws = AnalysisDataService.retrieve(raw_ws)
+ else:
+ matrix_ws = raw_ws
+ assert isinstance(matrix_ws, mantid.dataobjects.Workspace2D)
+
+ self._myRawDataWSDict[(exp_no, scan_no, pt_no)] = matrix_ws
+
+ return
+
+ def _add_md_workspace(self, exp_no, scan_no, pt_no, md_ws):
+ """
+ Add MD workspace to storage
+ :param exp_no:
+ :param scan_no:
+ :param pt_no:
+ :param md_ws:
+ :return:
+ """
+ # Check input
+ print '[DB] Type of md_ws is %s.' % str(type(md_ws))
+ assert isinstance(md_ws, mantid.dataobjects.MDEventWorkspace)
+
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(pt_no)
+
+ self._myPtMDDict[(exp_no, scan_no, pt_no)] = md_ws
+
+ return
+
+ def _add_ub_peak_ws(self, exp_number, scan_number, pt_number, peak_ws):
+ """
+ Add peak workspace for UB matrix
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :param peak_ws:
+ :return:
+ """
+ # Check
+ assert isinstance(peak_ws, mantid.dataobjects.PeaksWorkspace)
+
+ assert isinstance(exp_number, int)
+ assert isinstance(scan_number, int)
+ assert isinstance(pt_number, int)
+
+ # Add
+ self._myUBPeakWSDict[(exp_number, scan_number, pt_number)] = peak_ws
+
+ return
+
+ def _add_spice_workspace(self, exp_no, scan_no, spice_table_ws):
+ """
+ """
+ assert isinstance(exp_no, int)
+ assert isinstance(scan_no, int)
+ assert isinstance(spice_table_ws, mantid.dataobjects.TableWorkspace)
+ self._mySpiceTableDict[(exp_no, scan_no)] = spice_table_ws
+
+ return
+
+ def _get_spice_workspace(self, exp_no, scan_no):
+ """ Get SPICE's scan table workspace
+ :param exp_no:
+ :param scan_no:
+ :return: Table workspace or None
+ """
+ try:
+ ws = self._mySpiceTableDict[(exp_no, scan_no)]
+ except KeyError:
+ print '[DB] Keys to SPICE TABLE: %s' % str(self._mySpiceTableDict.keys())
+ return None
+
+ return ws
+
+ def get_raw_data_workspace(self, exp_no, scan_no, pt_no):
+ """ Get raw workspace
+ """
+ try:
+ ws = self._myRawDataWSDict[(exp_no, scan_no, pt_no)]
+ assert isinstance(ws, mantid.dataobjects.Workspace2D)
+ except KeyError:
+ return None
+
+ return ws
+
+ def _get_pt_list_from_spice_table(self, spice_table_ws):
+ """
+ Get list of Pt. from a SPICE table workspace
+ :param spice_table_ws: SPICE table workspace
+ :return: list of Pt.
+ """
+ numrows = spice_table_ws.rowCount()
+ ptlist = []
+ for irow in xrange(numrows):
+ ptno = int(spice_table_ws.cell(irow, 0))
+ ptlist.append(ptno)
+
+ return ptlist
+
+
+def get_spice_file_name(exp_number, scan_number):
+ """
+ Get standard HB3A SPICE file name from experiment number and scan number
+ :param exp_number:
+ :param scan_num:
+ :return:
+ """
+ file_name = 'HB3A_exp%04d_scan%04d.dat' % (exp_number, scan_number)
+
+ return file_name
+
+
+def get_spice_table_name(exp_number, scan_number):
+ """ Form the name of the table workspace for SPICE
+ :param exp_number:
+ :param scan_number:
+ :return:
+ """
+ table_name = 'HB3A_%03d_%04d_SpiceTable' % (exp_number, scan_number)
+
+ return table_name
+
+
+def get_raw_data_workspace_name(exp_number, scan_number, pt_number):
+ """ Form the name of the matrix workspace to which raw pt. XML file is loaded
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'HB3A_exp%d_scan%04d_%04d' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_pt_info_ws_name(exp_number, scan_number):
+ """
+ Information table workspace'name from CollectHB3AInfo
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'ScanPtInfo_Exp%d_Scan%d' % (exp_number, scan_number)
+
+ return ws_name
+
+
+def get_single_pt_peak_ws_name(exp_number, scan_number, pt_number):
+ """
+ Form the name of the peak workspace
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'Peak_Exp%d_Scan%d_Pt%d' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_single_pt_md_name(exp_number, scan_number, pt_number):
+ """ Form the name of the MDEvnetWorkspace for a single Pt. measurement
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'HB3A_Exp%d_Scan%d_Pt%d_MD' % (exp_number, scan_number, pt_number)
+
+ return ws_name
+
+
+def get_virtual_instrument_table_name(exp_number, scan_number, pt_number):
+ """
+ Generate the name of the table workspace containing the virtual instrument information
+ :param exp_number:
+ :param scan_number:
+ :param pt_number:
+ :return:
+ """
+ ws_name = 'VirtualInstrument_Exp%d_Scan%d_Pt%d_Table' % (exp_number, scan_number, pt_number)
+
+ return ws_name
diff --git a/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
new file mode 100644
index 0000000000000000000000000000000000000000..7009c1e8b8ec763ec515120f212242332cf5e2b9
--- /dev/null
+++ b/scripts/HFIR_4Circle_Reduction/reduce4circleGUI.py
@@ -0,0 +1,1092 @@
+#pylint: disable=invalid-name,relative-import,W0611,R0921,R0902,R0904,R0921,C0302
+################################################################################
+#
+# MainWindow application for reducing HFIR 4-circle
+#
+################################################################################
+import os
+import math
+import csv
+import time
+
+from PyQt4 import QtCore, QtGui
+
+import reduce4circleControl as r4c
+import guiutility as gutil
+import fourcircle_utility as fcutil
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ def _fromUtf8(s):
+ return s
+
+# import line for the UI python class
+from ui_MainWindow import Ui_MainWindow
+
+
+class MainWindow(QtGui.QMainWindow):
+ """ Class of Main Window (top)
+ """
+ def __init__(self, parent=None):
+ """ Initialization and set up
+ """
+ # Base class
+ QtGui.QMainWindow.__init__(self,parent)
+
+ # UI Window (from Qt Designer)
+ self.ui = Ui_MainWindow()
+ self.ui.setupUi(self)
+
+ # Mantid configuration
+ self._instrument = str(self.ui.comboBox_instrument.currentText())
+ # config = ConfigService.Instance()
+ # self._instrument = config["default.instrument"]
+
+ # Event handling definitions
+ # Top
+ self.connect(self.ui.pushButton_setExp, QtCore.SIGNAL('clicked()'),
+ self.do_set_experiment)
+
+ # Tab 'Data Access'
+ self.connect(self.ui.pushButton_applySetup, QtCore.SIGNAL('clicked()'),
+ self.do_apply_setup)
+ self.connect(self.ui.pushButton_browseLocalDataDir, QtCore.SIGNAL('clicked()'),
+ self.do_browse_local_spice_data)
+ self.connect(self.ui.pushButton_testURLs, QtCore.SIGNAL('clicked()'),
+ self.do_test_url)
+ self.connect(self.ui.pushButton_ListScans, QtCore.SIGNAL('clicked()'),
+ self.do_list_scans)
+ self.connect(self.ui.pushButton_downloadExpData, QtCore.SIGNAL('clicked()'),
+ self.do_download_spice_data)
+ self.connect(self.ui.comboBox_mode, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.change_data_access_mode)
+
+ # Tab 'View Raw Data'
+ self.connect(self.ui.pushButton_setScanInfo, QtCore.SIGNAL('clicked()'),
+ self.do_load_scan_info)
+ self.connect(self.ui.pushButton_plotRawPt, QtCore.SIGNAL('clicked()'),
+ self.do_plot_pt_raw)
+ self.connect(self.ui.pushButton_prevPtNumber, QtCore.SIGNAL('clicked()'),
+ self.do_plot_prev_pt_raw)
+ self.connect(self.ui.pushButton_nextPtNumber, QtCore.SIGNAL('clicked()'),
+ self.do_plot_next_pt_raw)
+ self.connect(self.ui.pushButton_showPtList, QtCore.SIGNAL('clicked()'),
+ self.show_scan_pt_list)
+ self.connect(self.ui.pushButton_usePt4UB, QtCore.SIGNAL('clicked()'),
+ self.do_add_peak_to_find)
+
+ # Tab 'calculate ub matrix'
+ self.connect(self.ui.pushButton_findPeak, QtCore.SIGNAL('clicked()'),
+ self.do_find_peak)
+ self.connect(self.ui.pushButton_addPeakToCalUB, QtCore.SIGNAL('clicked()'),
+ self.do_add_ub_peak)
+ self.connect(self.ui.pushButton_calUB, QtCore.SIGNAL('clicked()'),
+ self.do_cal_ub_matrix)
+ self.connect(self.ui.pushButton_acceptUB, QtCore.SIGNAL('clicked()'),
+ self.doAcceptCalUB)
+ self.connect(self.ui.pushButton_indexUBPeaks, QtCore.SIGNAL('clicked()'),
+ self.do_index_ub_peaks)
+ self.connect(self.ui.pushButton_deleteUBPeak, QtCore.SIGNAL('clicked()'),
+ self.do_del_ub_peaks)
+ self.connect(self.ui.pushButton_clearUBPeakTable, QtCore.SIGNAL('clicked()'),
+ self.do_clear_ub_peaks)
+ self.connect(self.ui.pushButton_resetPeakHKLs, QtCore.SIGNAL('clicked()'),
+ self.do_reset_ub_peaks_hkl)
+
+ # Tab 'Slice View'
+ self.connect(self.ui.pushButton_setUBSliceView, QtCore.SIGNAL('clicked()'),
+ self.do_set_ub_sv)
+ self.connect(self.ui.pushButton_process4SliceView, QtCore.SIGNAL('clicked()'),
+ self.do_merge_scans)
+
+ # Tab 'Advanced'
+ self.connect(self.ui.pushButton_useDefaultDir, QtCore.SIGNAL('clicked()'),
+ self.do_setup_dir_default)
+ self.connect(self.ui.pushButton_browseLocalCache, QtCore.SIGNAL('clicked()'),
+ self.do_browse_local_cache_dir)
+ self.connect(self.ui.pushButton_browseWorkDir, QtCore.SIGNAL('clicked()'),
+ self.do_browse_working_dir)
+ self.connect(self.ui.comboBox_instrument, QtCore.SIGNAL('currentIndexChanged(int)'),
+ self.change_instrument_name)
+
+ # Refine UB matrix
+ self.connect(self.ui.pushButton_addToRefine, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_addAllRefineUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_acceptRefinedUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+ self.connect(self.ui.pushButton_resetRefinedUB, QtCore.SIGNAL('clicked()'),
+ self.do_refine_ub)
+
+ # Tab 'Integrate Peaks'
+ self.connect(self.ui.pushButton_integratePeak, QtCore.SIGNAL('clicked()'),
+ self.do_integrate_peaks)
+
+ # Menu
+ self.connect(self.ui.actionExit, QtCore.SIGNAL('triggered()'),
+ self.menu_quit)
+
+ self.connect(self.ui.actionSave_Session, QtCore.SIGNAL('triggered()'),
+ self.save_current_session)
+ self.connect(self.ui.actionLoad_Session, QtCore.SIGNAL('triggered()'),
+ self.load_session)
+
+ # Event handling for tab 'refine ub matrix'
+ self.connect(self.ui.pushButton_addToRefine, QtCore.SIGNAL('clicked()'),
+ self.doAddScanPtToRefineUB)
+
+ # Validator ... (NEXT)
+
+ # Declaration of class variable
+ # some configuration
+ self._homeSrcDir = os.getcwd()
+ self._homeDir = os.getcwd()
+
+ # Control
+ self._myControl = r4c.CWSCDReductionControl(self._instrument)
+ self._allowDownload = True
+ self._dataAccessMode = 'Download'
+
+ # Initial setup
+ self.ui.tabWidget.setCurrentIndex(0)
+ self.ui.tabWidget.setTabEnabled(4, False)
+ self.ui.tabWidget.setTabEnabled(5, False)
+ self._init_ub_table()
+ self.ui.radioButton_ubFromTab1.setChecked(True)
+
+ # Tab 'Access'
+ self.ui.lineEdit_url.setText('http://neutron.ornl.gov/user_data/hb3a/')
+ self.ui.comboBox_mode.setCurrentIndex(0)
+ self.ui.lineEdit_localSpiceDir.setEnabled(True)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(True)
+
+ return
+
+ def do_integrate_peaks(self):
+ """
+
+ :return:
+ """
+ raise RuntimeError('ASAP')
+
+ def do_refine_ub(self):
+ """
+
+ :return:
+ """
+ raise RuntimeError('Next Release')
+
+ def _init_ub_table(self):
+ """ DOC
+ :return:
+ """
+ # UB-peak table
+ # NOTE: have to call this because pyqt set column and row to 0 after __init__
+ # thus a 2-step initialization has to been adopted
+ self.ui.tableWidget_peaksCalUB.setup()
+
+ self.ui.tableWidget_ubMatrix.setup()
+ self.ui.tableWidget_ubSiceView.setup()
+ self.ui.tableWidget_refinedUB.setup()
+
+ self.ui.tableWidget_sliceViewProgress.setup()
+
+ return
+
+ def change_data_access_mode(self):
+ """ Change data access mode between downloading from server and local
+ Event handling methods
+ :return:
+ """
+ new_mode = str(self.ui.comboBox_mode.currentText())
+ self._dataAccessMode = new_mode
+
+ if new_mode.startswith('Local') is True:
+ self.ui.lineEdit_localSpiceDir.setEnabled(True)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(True)
+ self.ui.lineEdit_url.setEnabled(False)
+ self.ui.lineEdit_localSrcDir.setEnabled(False)
+ self.ui.pushButton_browseLocalCache.setEnabled(False)
+ self._allowDownload = False
+ else:
+ self.ui.lineEdit_localSpiceDir.setEnabled(False)
+ self.ui.pushButton_browseLocalDataDir.setEnabled(False)
+ self.ui.lineEdit_url.setEnabled(True)
+ self.ui.lineEdit_localSrcDir.setEnabled(True)
+ self.ui.pushButton_browseLocalCache.setEnabled(True)
+ self._allowDownload = True
+
+ return
+
+ def change_instrument_name(self):
+ """ Handing the event as the instrument name is changed
+ :return:
+ """
+ new_instrument = str(self.ui.comboBox_instrument.currentText())
+ self.pop_one_button_dialog('Change of instrument during data processing is dangerous.')
+ status, error_message = self._myControl.set_instrument_name(new_instrument)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+
+ return
+
+ def do_add_ub_peak(self):
+ """ Add current to ub peaks
+ :return:
+ """
+ # Add peak
+ status, int_list = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_scanNumber,
+ self.ui.lineEdit_ptNumber])
+ if status is False:
+ self.pop_one_button_dialog(int_list)
+ exp_no, scan_no, pt_no = int_list
+
+ # Get HKL from GUI
+ status, float_list = gutil.parse_float_editors([self.ui.lineEdit_H,
+ self.ui.lineEdit_K,
+ self.ui.lineEdit_L])
+ if status is False:
+ err_msg = float_list
+ self.pop_one_button_dialog(err_msg)
+ return
+ h, k, l = float_list
+
+ status, peak_info_obj = self._myControl.get_peak_info(exp_no, scan_no, pt_no)
+ if status is False:
+ error_message = peak_info_obj
+ self.pop_one_button_dialog(error_message)
+ return
+ assert isinstance(peak_info_obj, r4c.PeakInfo)
+
+ if self.ui.checkBox_roundHKLInt.isChecked():
+ h = math.copysign(1, h)*int(abs(h)+0.5)
+ k = math.copysign(1, k)*int(abs(k)+0.5)
+ l = math.copysign(1, l)*int(abs(l)+0.5)
+ peak_info_obj.set_user_hkl(h, k, l)
+ self.set_ub_peak_table(peak_info_obj)
+
+ # Clear
+ self.ui.lineEdit_scanNumber.setText('')
+ self.ui.lineEdit_ptNumber.setText('')
+
+ self.ui.lineEdit_sampleQx.setText('')
+ self.ui.lineEdit_sampleQy.setText('')
+ self.ui.lineEdit_sampleQz.setText('')
+
+ self.ui.lineEdit_H.setText('')
+ self.ui.lineEdit_K.setText('')
+ self.ui.lineEdit_L.setText('')
+
+ return
+
+ def doAcceptCalUB(self):
+ """ Accept the calculated UB matrix
+ """
+ raise RuntimeError('ASAP')
+ return
+
+ def doAddScanPtToRefineUB(self):
+ """ Add scan/pt numbers to the list of data points for refining ub matrix
+
+ And the added scan number and pt numbers will be reflected in the (left sidebar)
+
+ """
+ raise RuntimeError("ASAP")
+
+ def do_add_peak_to_find(self):
+ """
+ Add the scan/pt to the next
+ :return:
+ """
+ scan_no = self.ui.lineEdit_run.text()
+ pt_no = self.ui.lineEdit_rawDataPtNo.text()
+
+ self.ui.lineEdit_scanNumber.setText(scan_no)
+ self.ui.lineEdit_ptNumber.setText(pt_no)
+
+ self.ui.tabWidget.setCurrentIndex(2)
+
+ def do_browse_local_cache_dir(self):
+ """ Browse local cache directory
+ :return:
+ """
+ local_cache_dir = str(QtGui.QFileDialog.getExistingDirectory(self,
+ 'Get Local Cache Directory',
+ self._homeSrcDir))
+
+ # Set local directory to control
+ status, error_message = self._myControl.set_local_data_dir(local_cache_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Synchronize to local data/spice directory and local cache directory
+ if str(self.ui.lineEdit_localSpiceDir.text()) != '':
+ prev_dir = str(self.ui.lineEdit_localSrcDir.text())
+ self.pop_one_button_dialog('Local data directory was set up as %s' %
+ prev_dir)
+ self.ui.lineEdit_localSrcDir.setText(local_cache_dir)
+ self.ui.lineEdit_localSpiceDir.setText(local_cache_dir)
+
+ return
+
+ def do_browse_local_spice_data(self):
+ """ Browse local source SPICE data directory
+ """
+ src_spice_dir = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Directory',
+ self._homeSrcDir))
+ # Set local data directory to controller
+ status, error_message = self._myControl.set_local_data_dir(src_spice_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ self._homeSrcDir = src_spice_dir
+ self.ui.lineEdit_localSpiceDir.setText(src_spice_dir)
+
+ return
+
+ def do_browse_working_dir(self):
+ """
+ Browse and set up working directory
+ :return:
+ """
+ work_dir = str(QtGui.QFileDialog.getExistingDirectory(self, 'Get Working Directory', self._homeDir))
+ status, error_message = self._myControl.set_working_directory(work_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ else:
+ self.ui.lineEdit_workDir.setText(work_dir)
+
+ return
+
+ def do_cal_ub_matrix(self):
+ """ Calculate UB matrix by 2 or 3 reflections
+ """
+ # Get reflections
+ num_rows = self.ui.tableWidget_peaksCalUB.rowCount()
+ peak_info_list = list()
+ status, exp_number = gutil.parse_integers_editors(self.ui.lineEdit_exp)
+ for i_row in xrange(num_rows):
+ if self.ui.tableWidget_peaksCalUB.is_selected(i_row) is True:
+ scan_num, pt_num = self.ui.tableWidget_peaksCalUB.get_exp_info(i_row)
+ status, peak_info = self._myControl.get_peak_info(exp_number, scan_num, pt_num)
+ peak_info.set_peak_ws_hkl_from_user()
+ if status is False:
+ self.pop_one_button_dialog(peak_info)
+ return
+ assert isinstance(peak_info, r4c.PeakInfo)
+ peak_info_list.append(peak_info)
+ # END-FOR
+
+ # Get lattice
+ status, ret_obj = self._get_lattice_parameters()
+ if status is True:
+ a, b, c, alpha, beta, gamma = ret_obj
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog(err_msg)
+ return
+
+ # Calculate UB matrix
+ status, ub_matrix = self._myControl.calculate_ub_matrix(peak_info_list, a, b, c,
+ alpha, beta, gamma)
+
+ # Deal with result
+ if status is True:
+ self._show_ub_matrix(ub_matrix)
+ else:
+ err_msg = ub_matrix
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_clear_ub_peaks(self):
+ """
+ Clear all peaks in UB-Peak table
+ :return:
+ """
+ self.ui.tableWidget_peaksCalUB.clear()
+
+ return
+
+ def do_del_ub_peaks(self):
+ """
+ Delete a peak in UB-Peak table
+ :return:
+ """
+ # Find out the lines to get deleted
+ row_num_list = self.ui.tableWidget_peaksCalUB.get_selected_rows()
+ print '[DB] Row %s are selected' % str(row_num_list)
+
+ # Delete
+ self.ui.tableWidget_peaksCalUB.delete_rows(row_num_list)
+
+ return
+
+ def do_download_spice_data(self):
+ """ Download SPICE data
+ :return:
+ """
+ # Check scans to download
+ scan_list_str = str(self.ui.lineEdit_downloadScans.text())
+ if len(scan_list_str) > 0:
+ # user specifies scans to download
+ valid, scan_list = fcutil.parse_int_array(scan_list_str)
+ if valid is False:
+ error_message = scan_list
+ self.pop_one_button_dialog(error_message)
+ else:
+ # Get all scans
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp])
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ return
+ exp_no = ret_obj
+ assert isinstance(exp_no, int)
+ server_url = str(self.ui.lineEdit_url.text())
+ scan_list = fcutil.get_scans_list(server_url, exp_no, return_list=True)
+ self.pop_one_button_dialog('Going to download scans %s.' % str(scan_list))
+
+ # Check location
+ destination_dir = str(self.ui.lineEdit_localSrcDir.text())
+ status, error_message = self._myControl.set_local_data_dir(destination_dir)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ else:
+ self.pop_one_button_dialog('Spice files will be downloaded to %s.' % destination_dir)
+
+ # Set up myControl for downloading data
+ exp_no = int(self.ui.lineEdit_exp.text())
+ self._myControl.set_exp_number(exp_no)
+
+ server_url = str(self.ui.lineEdit_url.text())
+ status, error_message = self._myControl.set_server_url(server_url)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Download
+ self._myControl.download_data_set(scan_list)
+
+ return
+
+ def do_find_peak(self):
+ """ Find peak in a given scan/pt and record it
+ """
+ # Get experiment, scan and pt
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_scanNumber,
+ self.ui.lineEdit_ptNumber])
+ if status is True:
+ exp_no, scan_no, pt_no = ret_obj
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Find peak
+ status, err_msg = self._myControl.find_peak(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ return
+ if self.ui.checkBox_loadHKLfromFile.isChecked() is True:
+ # This is the first time that in the workflow to get HKL from MD workspace
+ status, err_msg = self._myControl.set_hkl_to_peak(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog('Unable to locate peak info due to %s.' % err_msg)
+
+ # Set up correct values to table tableWidget_peaksCalUB
+ self._myControl.add_peak_info(exp_no, scan_no, pt_no)
+ status, peak_info = self._myControl.get_peak_info(exp_no, scan_no, pt_no)
+ if status is False:
+ err_msg = peak_info
+ raise KeyError(err_msg)
+ assert isinstance(peak_info, r4c.PeakInfo)
+
+ # Set the HKL value from PeakInfo directly
+ # BAD PROGRAMMING! THERE ARE TOO MANY WAYS TO ACCESS STORED HKL
+ h, k, l = peak_info.get_peak_ws_hkl()
+ self.ui.lineEdit_H.setText('%.2f' % h)
+ self.ui.lineEdit_K.setText('%.2f' % k)
+ self.ui.lineEdit_L.setText('%.2f' % l)
+
+ q_sample = peak_info.getQSample()
+ self.ui.lineEdit_sampleQx.setText('%.5E' % q_sample[0])
+ self.ui.lineEdit_sampleQy.setText('%.5E' % q_sample[1])
+ self.ui.lineEdit_sampleQz.setText('%.5E' % q_sample[2])
+
+ # self.set_ub_peak_table(peak_info)
+
+ return
+
+ def do_index_ub_peaks(self):
+ """ Index the peaks in the UB matrix peak table
+ :return:
+ """
+ # Get UB matrix
+ ub_matrix = self.ui.tableWidget_ubMatrix.get_matrix()
+ print '[DB] Get UB matrix ', ub_matrix
+
+ # Do it for each peak
+ num_peaks = self.ui.tableWidget_peaksCalUB.rowCount()
+ err_msg = ''
+ for i_peak in xrange(num_peaks):
+ scan_no, pt_no = self.ui.tableWidget_peaksCalUB.get_exp_info(i_peak)
+ status, ret_obj = self._myControl.index_peak(ub_matrix, scan_number=scan_no,
+ pt_number=pt_no)
+ if status is True:
+ new_hkl = ret_obj[0]
+ error = ret_obj[1]
+ self.ui.tableWidget_peaksCalUB.set_hkl(i_peak, new_hkl, error)
+ else:
+ err_msg += ret_obj + '\n'
+ # END-FOR
+
+ if len(err_msg) > 0:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_list_scans(self):
+ """ List all scans available
+ :return:
+ """
+ # Experiment number
+ exp_no = int(self.ui.lineEdit_exp.text())
+
+ access_mode = str(self.ui.comboBox_mode.currentText())
+ if access_mode == 'Local':
+ spice_dir = str(self.ui.lineEdit_localSpiceDir.text())
+ message = fcutil.get_scans_list_local_disk(spice_dir, exp_no)
+ else:
+ url = str(self.ui.lineEdit_url.text())
+ message = fcutil.get_scans_list(url, exp_no)
+
+ self.pop_one_button_dialog(message)
+
+ return
+
+ def do_load_scan_info(self):
+ """ Load SIICE's scan file
+ :return:
+ """
+ # Get scan number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_run])
+ if status is True:
+ scan_no = ret_obj[0]
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog('Unable to get scan number in raw data tab due to %s.' % err_msg)
+ return
+
+ status, err_msg = self._myControl.load_spice_scan_file(exp_no=None, scan_no=scan_no)
+ if status is False:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def do_plot_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Call to plot 2D
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_plot_prev_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Previous one
+ pt_no -= 1
+ if pt_no <= 0:
+ self.pop_one_button_dialog('Pt. = 1 is the first one.')
+ return
+ else:
+ self.ui.lineEdit_rawDataPtNo.setText('%d' % pt_no)
+
+ # Plot
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_plot_next_pt_raw(self):
+ """ Plot the Pt.
+ """
+ # Get measurement pt and the file number
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp,
+ self.ui.lineEdit_run,
+ self.ui.lineEdit_rawDataPtNo])
+ if status is True:
+ exp_no = ret_obj[0]
+ scan_no = ret_obj[1]
+ pt_no = ret_obj[2]
+ else:
+ self.pop_one_button_dialog(ret_obj)
+ return
+
+ # Previous one
+ pt_no += 1
+ # get last Pt. number
+ status, last_pt_no = self._myControl.get_pt_numbers(exp_no, scan_no)
+ if status is False:
+ error_message = last_pt_no
+ self.pop_one_button_dialog('Unable to access Spice table for scan %d. Reason" %s.' % (
+ scan_no, error_message))
+ if pt_no > last_pt_no:
+ self.pop_one_button_dialog('Pt. = %d is the last one of scan %d.' % (pt_no, scan_no))
+ return
+ else:
+ self.ui.lineEdit_rawDataPtNo.setText('%d' % pt_no)
+
+ # Plot
+ self._plot_raw_xml_2d(exp_no, scan_no, pt_no)
+
+ return
+
+ def do_merge_scans(self):
+ """ Process data for slicing view
+ :return:
+ """
+ # Get UB matrix
+ ub_matrix = self.ui.tableWidget_ubSiceView.get_matrix()
+ self._myControl.set_ub_matrix(exp_number=None, ub_matrix=ub_matrix)
+
+ # Get list of scans
+ scan_list = gutil.parse_integer_list(str(self.ui.lineEdit_listScansSliceView.text()))
+ if len(scan_list) == 0:
+ self.pop_one_button_dialog('Scan list is empty.')
+
+ # Set table
+ self.ui.tableWidget_sliceViewProgress.append_scans(scans=scan_list)
+
+ # Warning
+ self.pop_one_button_dialog('Data processing is long. Be patient!')
+
+ # Process
+ base_name = str(self.ui.lineEdit_baseMergeMDName.text())
+ scan_list.sort()
+ frame = str(self.ui.comboBox_mergeScanFrame.currentText())
+ for scan_no in scan_list:
+ # Download/check SPICE file
+ self._myControl.download_spice_file(None, scan_no, over_write=False)
+
+ # Get some information
+ status, pt_list = self._myControl.get_pt_numbers(None, scan_no, load_spice_scan=True)
+ if status is False:
+ err_msg = pt_list
+ self.pop_one_button_dialog('Failed to get Pt. number: %s' % err_msg)
+ return
+ else:
+ # Set information to table
+ err_msg = self.ui.tableWidget_sliceViewProgress.set_scan_pt(scan_no, pt_list)
+ if len(err_msg) > 0:
+ self.pop_one_button_dialog(err_msg)
+
+ out_ws_name = base_name + '%04d' % scan_no
+ self.ui.tableWidget_sliceViewProgress.set_scan_pt(scan_no, 'In Processing')
+ try:
+ ret_tup = self._myControl.merge_pts_in_scan(exp_no=None, scan_no=scan_no,
+ target_ws_name=out_ws_name,
+ target_frame=frame)
+ merge_status = 'Done'
+ merged_name = ret_tup[0]
+ group_name = ret_tup[1]
+ except RuntimeError as e:
+ merge_status = 'Failed. Reason: %s' % str(e)
+ merged_name = ''
+ group_name = ''
+ finally:
+ self.ui.tableWidget_sliceViewProgress.set_status(scan_no, merge_status)
+ self.ui.tableWidget_sliceViewProgress.set_ws_names(scan_no, merged_name, group_name)
+
+ # Sleep for a while
+ time.sleep(0.1)
+ # END-FOR
+
+ return
+
+ def do_reset_ub_peaks_hkl(self):
+ """
+ Reset user specified HKL value to peak table
+ :return:
+ """
+ num_rows = self.ui.tableWidget_peaksCalUB.rowCount()
+ for i_row in xrange(num_rows):
+ print '[DB] Update row %d' % (i_row)
+ scan, pt = self.ui.tableWidget_peaksCalUB.get_scan_pt(i_row)
+ status, peak_info = self._myControl.get_peak_info(None, scan, pt)
+ if status is False:
+ error_message = peak_info
+ raise RuntimeError(error_message)
+ h, k, l = peak_info.get_user_hkl()
+ self.ui.tableWidget_peaksCalUB.update_hkl(i_row, h, k, l)
+ # END-FOR
+
+ return
+
+ def do_set_experiment(self):
+ """ Set experiment
+ :return:
+ """
+ status, ret_obj = gutil.parse_integers_editors([self.ui.lineEdit_exp])
+ if status is True:
+ exp_number = ret_obj[0]
+ curr_exp_number = self._myControl.get_experiment()
+ if curr_exp_number is not None and exp_number != curr_exp_number:
+ self.pop_one_button_dialog('Changing experiment to %d. Clean previous experiment %d\'s result'
+ ' in Mantid manually.' % (exp_number, curr_exp_number))
+ self._myControl.set_exp_number(exp_number)
+ self.ui.lineEdit_exp.setStyleSheet('color: black')
+ else:
+ err_msg = ret_obj
+ self.pop_one_button_dialog('Unable to set experiment as %s' % err_msg)
+ self.ui.lineEdit_exp.setStyleSheet('color: red')
+
+ self.ui.tabWidget.setCurrentIndex(0)
+
+ return
+
+ def do_set_ub_sv(self):
+ """ Set UB matrix in Slice view
+ :return:
+ """
+ if self.ui.radioButton_ubFromTab1.isChecked():
+ self.ui.tableWidget_ubSiceView.set_from_matrix(self.ui.tableWidget_ubMatrix.get_matrix())
+ elif self.ui.radioButton_ubFromTab3.isChecked():
+ self.ui.tableWidget_ubSiceView.set_from_matrix(self.ui.tableWidget_refinedUB.get_matrix())
+ elif self.ui.radioButton_ubFromList.isChecked():
+ status, ret_obj = gutil.parse_float_array(str(self.ui.plainTextEdit_ubInput.toPlainText()))
+ if status is False:
+ self.pop_one_button_dialog(ret_obj)
+ elif len(ret_obj) != 9:
+ self.pop_one_button_dialog('Requiring 9 floats for UB matrix. Only %d are given.' % len(ret_obj))
+ else:
+ self.ui.tableWidget_ubSiceView.set_from_list(ret_obj)
+ else:
+ self.pop_one_button_dialog('None is selected to set UB matrix.')
+
+ return
+
+ def do_setup_dir_default(self):
+ """
+ Set up default directory for storing data and working
+ :return:
+ """
+ home_dir = os.path.expanduser('~')
+
+ # Data cache directory
+ data_cache_dir = os.path.join(home_dir, 'Temp/HB3ATest')
+ self.ui.lineEdit_localSpiceDir.setText(data_cache_dir)
+ self.ui.lineEdit_localSrcDir.setText(data_cache_dir)
+
+ work_dir = os.path.join(data_cache_dir, 'Workspace')
+ self.ui.lineEdit_workDir.setText(work_dir)
+
+ return
+
+ def do_apply_setup(self):
+ """
+ Apply set up ...
+ :return:
+ """
+ # Local data directory
+ local_data_dir = str(self.ui.lineEdit_localSpiceDir.text())
+ if os.path.exists(local_data_dir) is False:
+ try:
+ os.mkdir(local_data_dir)
+ except OSError as os_error:
+ self.pop_one_button_dialog('Unable to create local data directory %s due to %s.' % (
+ local_data_dir, str(os_error)))
+ self.ui.lineEdit_localSpiceDir.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_localSpiceDir.setStyleSheet("color: black;")
+ # END-IF
+
+ # Working directory
+ working_dir = str(self.ui.lineEdit_workDir.text())
+ if os.path.exists(working_dir) is False:
+ try:
+ os.mkdir(working_dir)
+ except OSError as os_error:
+ self.pop_one_button_dialog('Unable to create working directory %s due to %s.' % (
+ working_dir, str(os_error)))
+ self.ui.lineEdit_workDir.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_workDir.setStyleSheet("color: black;")
+ # END-IF
+
+ # Server URL
+ data_server = str(self.ui.lineEdit_url.text())
+ url_is_good = self.do_test_url()
+ if url_is_good is False:
+ self.ui.lineEdit_url.setStyleSheet("color: red;")
+ return
+ else:
+ self.ui.lineEdit_url.setStyleSheet("color: black;")
+
+ # Set to control
+ self._myControl.set_local_data_dir(local_data_dir)
+ self._myControl.set_working_directory(working_dir)
+ self._myControl.set_server_url(data_server)
+
+ return
+
+ def do_test_url(self):
+ """ Test whether the root URL provided specified is good
+ """
+ url = str(self.ui.lineEdit_url.text())
+
+ url_is_good, err_msg = fcutil.check_url(url)
+ if url_is_good is True:
+ self.pop_one_button_dialog("URL %s is valid." % url)
+ else:
+ self.pop_one_button_dialog(err_msg)
+
+ return url_is_good
+
+ def pop_one_button_dialog(self, message):
+ """ Pop up a one-button dialog
+ :param message:
+ :return:
+ """
+ assert isinstance(message, str)
+ QtGui.QMessageBox.information(self, '4-circle Data Reduction', message)
+
+ return
+
+ def save_current_session(self, filename=None):
+ """ Save current session/value setup to
+ :return:
+ """
+ # Set up dictionary
+ save_dict = dict()
+
+ # Setup
+ save_dict['lineEdit_localSpiceDir'] = str(self.ui.lineEdit_localSpiceDir.text())
+ save_dict['lineEdit_url'] = str(self.ui.lineEdit_url.text())
+ save_dict['lineEdit_workDir']= str(self.ui.lineEdit_workDir.text())
+
+ # Experiment
+ save_dict['lineEdit_exp'] = str(self.ui.lineEdit_exp.text())
+ save_dict['lineEdit_scanNumber'] = self.ui.lineEdit_scanNumber.text()
+ save_dict['lineEdit_ptNumber'] = str(self.ui.lineEdit_ptNumber.text())
+
+ # Lattice
+ save_dict['lineEdit_a'] = str(self.ui.lineEdit_a.text())
+ save_dict['lineEdit_b'] = str(self.ui.lineEdit_b.text())
+ save_dict['lineEdit_c'] = str(self.ui.lineEdit_c.text())
+ save_dict['lineEdit_alpha'] = str(self.ui.lineEdit_alpha.text())
+ save_dict['lineEdit_beta'] = str(self.ui.lineEdit_beta.text())
+ save_dict['lineEdit_gamma'] = str(self.ui.lineEdit_gamma.text())
+
+ # Merge scan
+ save_dict['plainTextEdit_ubInput'] = str(self.ui.plainTextEdit_ubInput.toPlainText())
+ save_dict['lineEdit_listScansSliceView'] = str(self.ui.lineEdit_listScansSliceView.text())
+ save_dict['lineEdit_baseMergeMDName'] = str(self.ui.lineEdit_baseMergeMDName.text())
+
+ # Save to csv file
+ if filename is None:
+ filename = 'session_backup.csv'
+ ofile = open(filename, 'w')
+ writer = csv.writer(ofile)
+ for key, value in save_dict.items():
+ writer.writerow([key, value])
+ ofile.close()
+
+ return
+
+ def load_session(self, filename=None):
+ """
+ To load a session, i.e., read it back:
+ :param filename:
+ :return:
+ """
+ if filename is None:
+ filename = 'session_backup.csv'
+
+ in_file = open(filename, 'r')
+ reader = csv.reader(in_file)
+ my_dict = dict(x for x in reader)
+
+ # ...
+ for key, value in my_dict.items():
+ if key.startswith('lineEdit') is True:
+ self.ui.__getattribute__(key).setText(value)
+ elif key.startswith('plainText') is True:
+ self.ui.__getattribute__(key).setPlainText(value)
+ elif key.startswith('comboBox') is True:
+ self.ui.__getattribute__(key).setCurrentIndex(int(value))
+ else:
+ self.pop_one_button_dialog('Error! Widget name %s is not supported' % key)
+ # END-FOR
+
+ # ...
+ self._myControl.set_local_data_dir(str(self.ui.lineEdit_localSpiceDir.text()))
+
+ return
+
+ def menu_quit(self):
+ """
+
+ :return:
+ """
+ self.close()
+
+ def show_scan_pt_list(self):
+ """ Show the range of Pt. in a scan
+ :return:
+ """
+ # Get parameters
+ status, inp_list = gutil.parse_integers_editors([self.ui.lineEdit_exp, self.ui.lineEdit_run])
+ if status is False:
+ self.pop_one_button_dialog(inp_list)
+ return
+ else:
+ exp_no = inp_list[0]
+ scan_no = inp_list[1]
+
+ status, ret_obj = self._myControl.get_pt_numbers(exp_no, scan_no)
+
+ # Form message
+ if status is False:
+ # Failed to get Pt. list
+ error_message = ret_obj
+ self.pop_one_button_dialog(error_message)
+ else:
+ # Form message
+ pt_list = sorted(ret_obj)
+ num_pts = len(pt_list)
+ info = 'Exp %d Scan %d has %d Pt. ranging from %d to %d.\n' % (exp_no, scan_no, num_pts,
+ pt_list[0], pt_list[-1])
+ num_miss_pt = pt_list[-1] - pt_list[0] + 1 - num_pts
+ if num_miss_pt > 0:
+ info += 'There are %d Pt. skipped.\n' % num_miss_pt
+
+ self.pop_one_button_dialog(info)
+
+ return
+
+ def set_ub_peak_table(self, peakinfo):
+ """
+ DOC
+ :param peak_info:
+ :return:
+ """
+ assert isinstance(peakinfo, r4c.PeakInfo)
+
+ # Get data
+ exp_number, scan_number, pt_number = peakinfo.getExpInfo()
+ h, k, l = peakinfo.get_user_hkl()
+ q_sample = peakinfo.getQSample()
+ m1 = self._myControl.get_sample_log_value(exp_number, scan_number, pt_number, '_m1')
+
+ # Set to table
+ status, err_msg = self.ui.tableWidget_peaksCalUB.append_row(
+ [scan_number, pt_number, h, k, l, q_sample[0], q_sample[1], q_sample[2], False, m1, ''])
+ if status is False:
+ self.pop_one_button_dialog(err_msg)
+
+ return
+
+ def _get_lattice_parameters(self):
+ """
+ Get lattice parameters from GUI
+ :return: (Boolean, Object). True, 6-tuple as a, b, c, alpha, beta, gamm
+ False: error message
+ """
+ status, ret_list = gutil.parse_float_editors([self.ui.lineEdit_a,
+ self.ui.lineEdit_b,
+ self.ui.lineEdit_c,
+ self.ui.lineEdit_alpha,
+ self.ui.lineEdit_beta,
+ self.ui.lineEdit_gamma])
+ if status is False:
+ err_msg = ret_list
+ err_msg = 'Unable to parse unit cell due to %s' % err_msg
+ return False, err_msg
+
+ a, b, c, alpha, beta, gamma = ret_list
+
+ return True, (a, b, c, alpha, beta, gamma)
+
+ def _plot_raw_xml_2d(self, exp_no, scan_no, pt_no):
+ """ Plot raw workspace from XML file for a measurement/pt.
+ """
+ # Check and load SPICE table file
+ does_exist = self._myControl.does_spice_loaded(exp_no, scan_no)
+ if does_exist is False:
+ # Download data
+ status, error_message = self._myControl.download_spice_file(exp_no, scan_no, over_write=False)
+ if status is True:
+ status, error_message = self._myControl.load_spice_scan_file(exp_no, scan_no)
+ if status is False and self._allowDownload is False:
+ self.pop_one_button_dialog(error_message)
+ return
+ else:
+ self.pop_one_button_dialog(error_message)
+ return
+ # END-IF(does_exist)
+
+ # Load Data for Pt's xml file
+ does_exist = self._myControl.does_raw_loaded(exp_no, scan_no, pt_no)
+
+ if does_exist is False:
+ # Check whether needs to download
+ status, error_message = self._myControl.download_spice_xml_file(scan_no, pt_no, exp_no=exp_no)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+ # Load SPICE xml file
+ status, error_message = self._myControl.load_spice_xml_file(exp_no, scan_no, pt_no)
+ if status is False:
+ self.pop_one_button_dialog(error_message)
+ return
+
+ # Convert a list of vector to 2D numpy array for imshow()
+ # Get data and plot
+ raw_det_data = self._myControl.get_raw_detector_counts(exp_no, scan_no, pt_no)
+ self.ui.graphicsView.clear_canvas()
+ self.ui.graphicsView.add_plot_2d(raw_det_data, x_min=0, x_max=256, y_min=0, y_max=256,
+ hold_prev_image=False)
+
+ return
+
+ def _show_ub_matrix(self, ubmatrix):
+ """ Show UB matrix
+ :param ubmatrix:
+ :return:
+ """
+ assert ubmatrix.shape == (3, 3)
+
+ self.ui.tableWidget_ubMatrix.set_from_matrix(ubmatrix)
+
+ return
diff --git a/scripts/Inelastic/Direct/DirectEnergyConversion.py b/scripts/Inelastic/Direct/DirectEnergyConversion.py
index 56043ad5aeed4096c76b402026bf270c95982230..74394d53c59d56718d782f4b99e3b56634f1a1f9 100644
--- a/scripts/Inelastic/Direct/DirectEnergyConversion.py
+++ b/scripts/Inelastic/Direct/DirectEnergyConversion.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from mantid.simpleapi import *
from mantid.kernel import funcreturns
diff --git a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index 624f599ba04d0e2848de1d7eae90cd134bcf83b3..f3c816ecbac11ce60b67842eb3f6dfbf1c4caad9 100644
--- a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -484,12 +484,12 @@ class MantidConfigDirectInelastic(object):
#
def init_user(self,fedIDorUser,theUser=None):
"""Define settings, specific to a user
- Supports two interfaces -- old and the new one
+ Supports two interfaces -- old and the new one
where
- OldInterface: requested two input parameters
+ OldInterface: requested two input parameters
fedID -- users federal id
theUser -- class defining all other user property
- NewInterface: requested single parameter:
+ NewInterface: requested single parameter:
theUser -- class defining all user's properties including fedID
"""
if not theUser:
diff --git a/scripts/Inelastic/Direct/PropertiesDescriptors.py b/scripts/Inelastic/Direct/PropertiesDescriptors.py
index f05779e6e22cb3be785e93284470526939658be8..aec0169cd240da45e7d63e5218902c7578eb579e 100644
--- a/scripts/Inelastic/Direct/PropertiesDescriptors.py
+++ b/scripts/Inelastic/Direct/PropertiesDescriptors.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
""" File contains collection of Descriptors used to define complex
properties in NonIDF_Properties and PropertyManager classes
diff --git a/scripts/Inelastic/Direct/RunDescriptor.py b/scripts/Inelastic/Direct/RunDescriptor.py
index 9fda6508d6224a370358ac200b8968be3aeca2c5..b5e959ff885084e6a088e0647532fa21445b65ca 100644
--- a/scripts/Inelastic/Direct/RunDescriptor.py
+++ b/scripts/Inelastic/Direct/RunDescriptor.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
""" File contains Descriptors used describe run for direct inelastic reduction """
@@ -995,8 +996,8 @@ class RunDescriptor(PropDescriptor):
Load(Filename=data_file, OutputWorkspace=ws_name,LoadMonitors = '1',MonitorsAsEvents='0')
#HACK >>> , necessary until #11565 is fixed
if nxs_file :
- instr_name = RunDescriptor._holder.instr_name
- if instr_name == 'LET' and self._run_number>14151 and self._run_number<14382:
+ instr_name = RunDescriptor._holder.instr_name
+ if instr_name == 'LET' and self._run_number>14151 and self._run_number<14382:
FrameworkManager.clearInstruments()
idf_file = api.ExperimentInfo.getInstrumentFilename(instr_name)
idf_path,tile = os.path.split(idf_file)
diff --git a/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py b/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
index 7140a4df5633e57ccaaca3b9719cc32474b3539f..abbd2f4eee91d7db012641d90db791d3ecdec1b6 100644
--- a/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
+++ b/scripts/Interface/reduction_gui/reduction/diffraction/diffraction_reduction_script.py
@@ -84,7 +84,7 @@ class DiffractionReductionScripter(BaseReductionScripter):
file_name, autosavexmlfname)
wbuf += script
wbuf += "\n========== End of Script ==========="
- print (wbuf)
+ print wbuf
return script
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
index ea324c63828a6e03190b8b2c5fc99b90bdf2fd80..72cfb428315fa574ee295ed307c2e1e696f1eb99 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name,unused-import
from PyQt4 import QtGui, QtCore
import reduction_gui.widgets.util as util
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py b/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
index bfb043368ad53ccaeb13b243a916cea1f8f5e615..8816e2f91ded5277314a7b6e267a8a72f8c424ac 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/refl_data_simple.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from PyQt4 import QtGui, uic, QtCore
import reduction_gui.widgets.util as util
diff --git a/scripts/Interface/ui/reflectometer/refl_gui.py b/scripts/Interface/ui/reflectometer/refl_gui.py
index 3bb3aed9b003789fd1786e1f1ecfa46f82878888..8f1a384733c2e605fd61b22f192b30ccc26b3b90 100644
--- a/scripts/Interface/ui/reflectometer/refl_gui.py
+++ b/scripts/Interface/ui/reflectometer/refl_gui.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
import ui_refl_window
import refl_save
diff --git a/scripts/Reflectometry/isis_reflectometry/procedures.py b/scripts/Reflectometry/isis_reflectometry/procedures.py
index 999dd0a65df4c3c69b2b8d82f085be1fa5d886ab..11d1a52448ec5749956eca3315db82a7a2537801 100644
--- a/scripts/Reflectometry/isis_reflectometry/procedures.py
+++ b/scripts/Reflectometry/isis_reflectometry/procedures.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from math import *
diff --git a/scripts/SANS/ISISCommandInterface.py b/scripts/SANS/ISISCommandInterface.py
index 0ed8fd805b698e6a5c35ffdf68ae9425299ed478..3f06b3229bf67e2a871806a1a62459c5db70707b 100644
--- a/scripts/SANS/ISISCommandInterface.py
+++ b/scripts/SANS/ISISCommandInterface.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
"""
Enables the SANS commands (listed at http://www.mantidproject.org/SANS) to
@@ -574,7 +575,7 @@ def _fitRescaleAndShift(rAnds, frontData, rearData):
# We need to make sure at this point that the workspaces are 1D. We
# don't really know how to match the workspaces for the 2D case.
- if (not su.is_1D_workspace(mtd[frontData]) or not su.is_1D_workspace(mtd[rearData])):
+ if not su.is_1D_workspace(mtd[frontData]) or not su.is_1D_workspace(mtd[rearData]):
sanslog.warning("Request to perform a fit to find the shift and scale values for"
"a non-1D workspace is not possible. Default values are provided.")
scale = rAnds.scale
diff --git a/scripts/SANS/SANSBatchMode.py b/scripts/SANS/SANSBatchMode.py
index 3419a9c6cd16d07aede08f6ca2a48e6918fb1d9b..38f01016a7b8b7744b9bdd942883cb8c133268b4 100644
--- a/scripts/SANS/SANSBatchMode.py
+++ b/scripts/SANS/SANSBatchMode.py
@@ -178,7 +178,8 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
original_settings = settings,
original_prop_man_settings = prop_man_settings)
except (RunTimeError, ValueError) as e:
- sanslog.warning("Error in Batchmode user files: Could not reset the specified user file %s. More info: %s" %(str(run['user_file']),str(e)))
+ sanslog.warning("Error in Batchmode user files: Could not reset the specified user file %s. More info: %s" %(
+ str(run['user_file']),str(e)))
local_settings = copy.deepcopy(ReductionSingleton().reference())
local_prop_man_settings = ReductionSingleton().settings.clone("TEMP_SETTINGS")
diff --git a/scripts/SANS/SANSUtility.py b/scripts/SANS/SANSUtility.py
index b22d9e8c19ad5d785f2d99beb9479be8769d5258..c594e7548e3d319888d9136a2b8c14c6831b8221 100644
--- a/scripts/SANS/SANSUtility.py
+++ b/scripts/SANS/SANSUtility.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
#########################################################
# This module contains utility functions common to the
diff --git a/scripts/SANS/isis_instrument.py b/scripts/SANS/isis_instrument.py
index b4c0a9a507d3bbcb0a063ac2c540d05a12eeb1ce..821b956195403a29bfb2b308d0a83d29286235c9 100644
--- a/scripts/SANS/isis_instrument.py
+++ b/scripts/SANS/isis_instrument.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
import math
import os
diff --git a/scripts/SANS/isis_reduction_steps.py b/scripts/SANS/isis_reduction_steps.py
index ebb89992488267b445b04ba4d1b5f16f99c55a98..f98175cf90062335d14d3cf0894e08d7e117e840 100644
--- a/scripts/SANS/isis_reduction_steps.py
+++ b/scripts/SANS/isis_reduction_steps.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
"""
This file defines what happens in each step in the data reduction, it's
diff --git a/scripts/reduction/instruments/reflectometer/wks_utility.py b/scripts/reduction/instruments/reflectometer/wks_utility.py
index b9dec721553ac63bdbeb835d613fe0b306a45bb4..7544a27a51147a23863c1579e17d2db0afac45d3 100644
--- a/scripts/reduction/instruments/reflectometer/wks_utility.py
+++ b/scripts/reduction/instruments/reflectometer/wks_utility.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines
#pylint: disable=invalid-name
from numpy import zeros, arctan2, arange, shape, sqrt, fliplr, asfarray, mean, sum, NAN
from mantid.simpleapi import *
diff --git a/tools/DOI/authors.py b/tools/DOI/authors.py
index aefa191509e7cae27eb14df35dfc91e564189b23..2d35b45b4aec8710fb2a8a7cff85ed3b137977e2 100644
--- a/tools/DOI/authors.py
+++ b/tools/DOI/authors.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from itertools import chain, ifilterfalse
import string, os, re
diff --git a/tools/DOI/doi.py b/tools/DOI/doi.py
index f27811292ed89caf678ee17b70bfcabae46b99a6..56c4a8782a92cef962d8e76cd0750eac47717d4d 100644
--- a/tools/DOI/doi.py
+++ b/tools/DOI/doi.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
"""A script for generating DataCite DOI's for Mantid releases, to be called by
a Jenkins job during the release process. When given a major, minor and patch
release number along with username and password credentials, it will build a
diff --git a/tools/DefaultConfigFiles/configToCpp.py b/tools/DefaultConfigFiles/configToCpp.py
index 6cd03a271650bc81ed2e03fcdc93110c0f563604..bb924e92af41df65efb48cf20fa26230099a49f7 100644
--- a/tools/DefaultConfigFiles/configToCpp.py
+++ b/tools/DefaultConfigFiles/configToCpp.py
@@ -7,8 +7,8 @@ import sys
with open(sys.argv[2]) as f:
for line in f:
- line = line.rstrip('\n')
- if line == "":
- print sys.argv[1] + " << std::endl;"
- else:
- print sys.argv[1] + " << \"" + line + "\" << std::endl;"
+ line = line.rstrip('\n')
+ if line == "":
+ print sys.argv[1] + " << std::endl;"
+ else:
+ print sys.argv[1] + " << \"" + line + "\" << std::endl;"
diff --git a/tools/PeriodicTable/generate_atom_code.py b/tools/PeriodicTable/generate_atom_code.py
index 6827ab0b10015a849b672f72dbc5f1b0c5c79780..3e2be400a0091c7ae44503bf0c060233302194e2 100755
--- a/tools/PeriodicTable/generate_atom_code.py
+++ b/tools/PeriodicTable/generate_atom_code.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
VERSION = "1.0"
diff --git a/tools/Pylint/fixPylint.py b/tools/Pylint/fixPylint.py
new file mode 100644
index 0000000000000000000000000000000000000000..5f3cf1d6990bde995780868418b7132eef3e4060
--- /dev/null
+++ b/tools/Pylint/fixPylint.py
@@ -0,0 +1,173 @@
+#pylint: disable=invalid-name,anomalous-backslash-in-string
+import os
+import re
+import argparse
+
+def fixBadIndent(toModify,indent):
+ err_string=indent.replace(' Bad indentation. Found ','').replace('(bad-indentation)','').split('spaces, expected')
+ bad=int(err_string[0])
+ good=int(err_string[1])
+ return toModify.replace(' '*bad,' '*good)
+
+def fixParens(fname,errorlist,errlines):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ newcontent=file_content
+ for i,error in zip(errlines,errorlist):
+ if error.find('(superfluous-parens)')!=-1:
+ kwd=error.split("'")[1]
+ pattern=re.compile(kwd+'(?P<spaces>\ *)\((?P<file_content>.*)\)')
+ match=pattern.search(file_content[i])
+ d=match.groupdict()
+ newcontent[i]=file_content[i].replace(kwd+d['spaces']+'('+d['file_content']+')',kwd+' '+d['file_content'])
+ tofixf=open(fname,'w')
+ tofixf.write(''.join(newcontent))
+ tofixf.close()
+
+def fixSeveralErrors(fname,errorlist,errlines):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ newcontent=file_content
+ for i,error in zip(errlines,errorlist):
+ if error.find('Bad indentation')!=-1:
+ newcontent[i]=fixBadIndent(file_content[i],error)
+ if error.find('missing-final-newline')!=-1:
+ newcontent[-1]+='\n'
+ if error.find('mixed-indentation')!=-1:
+ newcontent[i]=file_content[i].replace('\t', ' ')
+ if error.find('trailing-whitespace')!=-1:
+ newcontent[i]=file_content[i].rstrip()+'\n'
+ if error.find('Unnecessary semicolon')!=-1:
+ newcontent[i]=file_content[i].replace(';','')
+ tofixf=open(fname,'w')
+ tofixf.write(''.join(newcontent))
+ tofixf.close()
+
+def addIgnoreStatement(fname,errorlist):
+ tofixf=open(fname,'r')
+ file_content=tofixf.readlines()
+ tofixf.close()
+ ignore=[]
+ for error in errorlist:
+ if error.find('(invalid-name)')!=-1 and 'invalid-name' not in ignore:
+ ignore.append('invalid-name')
+ if error.find('(no-init)')!=-1 and 'no-init' not in ignore:
+ ignore.append('no-init')
+ if error.find('(too-many-lines)')!=-1 and 'too-many-lines' not in ignore:
+ ignore.append('too-many-lines')
+ if len(ignore)!=0:
+ tofixf=open(fname,'w')
+ tofixf.write("#pylint: disable="+','.join(ignore)+'\n')
+ tofixf.write(''.join(file_content))
+ tofixf.close()
+
+def generate_choices():
+ ch=['simple','parentheses','add_ignores']
+ ch_help=['simple - fixes the following warning: bad-indentation, missing-final-newline, '+\
+ 'mixed_indentation, trailing-whitespace, unnecesary-semicolon',
+ 'parentheses - fixes superfluous-parens warning',
+ 'add_ignores - adds ignore statemets at the beginning of each file to ignore invalid-name, no-init, too-many-lines']
+ chhelp="The possible choices supported are:\n\t"+'\n\t'.join(ch_help)
+ return (ch,chhelp)
+
+if __name__=='__main__':
+ choices,choices_help=generate_choices()
+ parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
+ epilog=choices_help,
+ description='Fix some pylint warnings. It is STRONGLY RECOMMENDED to '+\
+ 'rerun the pylintcheck between fixes')
+ parser.add_argument('-fix','--fix', default='simple',
+ choices=choices,
+ help='Select things to fix (default: simple). \nSee the choices options below.')
+ parser.add_argument('Filename', type=file, help='The output from "make pylint"')
+ parser.add_argument('-v','--version', action='version', version='%(prog)s 1.0')
+
+ #read pylint.log
+ args = parser.parse_args()
+ oneline=args.Filename.read()
+ args.Filename.close()
+ #ignore everything up to the first error
+ oneline=oneline[oneline.find('****'):]
+ content=oneline.split('\n')
+
+ fileindex=content.index('Checks of the following modules FAILED:')
+ files=[f.strip() for f in content[fileindex+1:-1]]
+ filenumber=0
+ linenumber=0
+ prevFile=True
+
+
+ while linenumber<fileindex:
+ filename=files[filenumber]
+ line=content[linenumber]
+ #find a file
+ if line.find('****')==0 and line.find('PyChop')==-1:
+ modname=line.split('************* Module ')[1]
+ if prevFile:
+ if os.path.isfile(filename):
+ correct_filename=filename
+ filenumber+=1
+ prevFile=True
+ else:
+ prevFile=False
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ else:
+ lastmodulename=os.path.split(filename)[1]
+ modbase=modname.split('.')[0]
+ if lastmodulename==modbase: #still in the same module
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ else: #go to the next file or module
+ filenumber+=1
+ filename=files[filenumber]
+ prevFile=True
+ if os.path.isfile(filename):
+ correct_filename=filename
+ filenumber+=1
+ prevFile=True
+ else:
+ prevFile=False
+ modname=modname.replace('.','/')
+ firstslash=modname.find('/')
+ if firstslash==-1:
+ correct_filename=filename+'/__init__.py'
+ else:
+ correct_filename=filename+modname[firstslash:]+'.py'
+ #process it
+ j=1
+ errors=[]
+ errorlines=[]
+ while linenumber+j<fileindex and content[linenumber+j].find('****')==-1:
+ err=content[linenumber+j]
+ if len(err)>0 and err[0] in ['C','W','E'] and err[1]==':':
+ lineNumber=int(err.split(':')[1].split(',')[0])-1
+ errors.append(err.split(':')[2])
+ errorlines.append(lineNumber)
+ j+=1
+ if args.fix=='simple':
+ fixSeveralErrors(correct_filename,errors,errorlines)
+ elif args.fix=='add_ignores':
+ addIgnoreStatement(correct_filename,errors)
+ elif args.fix=='parentheses':
+ fixParens(correct_filename,errors,errorlines)
+ linenumber+=j-1
+ else:
+ linenumber+=1
+
+
+
+
+
+
+
diff --git a/tools/Pylint/pylint.cfg b/tools/Pylint/pylint.cfg
index eec53d4f7b22bdfd67bc5e8f1c30b956fa6be060..cbf3bb4a69987805eca098774a89baba10598196 100644
--- a/tools/Pylint/pylint.cfg
+++ b/tools/Pylint/pylint.cfg
@@ -57,7 +57,7 @@ disable=W0142,I0011,F0401,W0614,E0602,C0111,C0326,W0401,R0201,R0801
output-format=colorized
# Include message's id in output
-include-ids=yes
+#include-ids=yes
# Put messages in a separate file for each module / package specified on the
# command line instead of printing them on stdout. Reports (if any) will be
diff --git a/tools/Pylint/run_pylint.py b/tools/Pylint/run_pylint.py
index 2b51de4194665b59e36f43166812cdb728a1b6c4..8368854c1fcafe1db6c7f464b3fe0a61a6f7922b 100644
--- a/tools/Pylint/run_pylint.py
+++ b/tools/Pylint/run_pylint.py
@@ -57,7 +57,7 @@ class Results(object):
"""
Return true if all files were clean
"""
- return (len(self.failures) == 0)
+ return len(self.failures) == 0
def add(self, modulename, status):
"""
@@ -172,8 +172,8 @@ def parse_arguments(argv):
help="If provided, store the output in the given file.")
parser.add_option("-x", "--exclude", dest="exclude", metavar="EXCLUDES",
help="If provided, a space-separated list of "
- "files/directories to exclude. Relative paths are "
- "taken as relative to --basedir")
+ "files/directories to exclude. Relative paths are "
+ "taken as relative to --basedir")
parser.set_defaults(format=DEFAULT_PYLINT_FORMAT, exe=DEFAULT_PYLINT_EXE, nofail=False,
basedir=os.getcwd(), rcfile=DEFAULT_RCFILE, exclude="")
@@ -242,6 +242,7 @@ def check_module_imports():
str: String indicating success/failure
"""
msg = ""
+ #pylint: disable=unused-variable
try:
import mantid
except ImportError, exc:
@@ -292,7 +293,7 @@ def run_checks(targets, serializer, options):
targetpath = os.path.join(options.basedir, target)
pkg_init = os.path.join(targetpath, "__init__.py")
if os.path.isfile(targetpath) or os.path.isfile(pkg_init):
- overall_stats.add(target, exec_pylint_on_importable(targetpath, serializer, options))
+ overall_stats.add(targetpath, exec_pylint_on_importable(targetpath, serializer, options))
else:
overall_stats.update(exec_pylint_on_all(targetpath, serializer, options, excludes))
##
@@ -352,7 +353,7 @@ def find_importable_targets(dirpath):
pkg_init = os.path.join(abspath, "__init__.py")
if (os.path.isfile(abspath) and item.endswith(".py")) or \
os.path.isfile(pkg_init):
- importables.append(abspath)
+ importables.append(abspath)
elif os.path.isdir(abspath):
importables.extend(package_walk(abspath))
return importables
@@ -386,7 +387,7 @@ def exec_pylint_on_importable(srcpath, serializer, options):
with temp_dir_change(os.path.dirname(srcpath)):
status = subp.call(cmd, stdout=serializer)
- return (status == 0)
+ return status == 0
#------------------------------------------------------------------------------
diff --git a/tools/TestViewer/TestViewer.py b/tools/TestViewer/TestViewer.py
index 428762ca8577534af6bc5449a80c9e08df2360d4..987819601d5c954e4bb51b9a0ce43707c03fdf91 100755
--- a/tools/TestViewer/TestViewer.py
+++ b/tools/TestViewer/TestViewer.py
@@ -4,4 +4,4 @@
""" Launch the GUI Test Viewer """
import main_window
-main_window.start()
\ No newline at end of file
+main_window.start()
diff --git a/tools/TestViewer/main_window.py b/tools/TestViewer/main_window.py
index 4117295fdb6b377a07b42355098a97c15d4e2bf9..48975b55710a5871b9c86f8211cbe22a839e7ebc 100644
--- a/tools/TestViewer/main_window.py
+++ b/tools/TestViewer/main_window.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
# -*- coding: utf-8 -*-
diff --git a/tools/TestViewer/test_info.py b/tools/TestViewer/test_info.py
index c43fb05c0cf7a6b8ba340dea515ec46d1c5643cf..e93f07021bebedf3cb17b4ab1e53fe6281c46a4f 100644
--- a/tools/TestViewer/test_info.py
+++ b/tools/TestViewer/test_info.py
@@ -1,3 +1,4 @@
+#pylint: disable=too-many-lines,invalid-name
# -*- coding: utf-8 -*-
""" Classes describing test projects,
how they are run,
@@ -77,7 +78,7 @@ class TestResult:
def __eq__(self, other):
""" Equality comparison """
if isinstance(other, TestResult):
- return ((self.value == other.value) and (self.old == other.old))
+ return (self.value == other.value) and (self.old == other.old)
else:
return self.value == other
@@ -372,7 +373,7 @@ class TestSuite(object):
self.contents_changed = True
else:
for i in xrange(len(self.tests)):
- if (self.tests[i].name != other.tests[i].name):
+ if self.tests[i].name != other.tests[i].name:
self.contents_changed = True
self.tests[i].replace_contents( other.tests[i] )
# Copy local values
@@ -402,7 +403,7 @@ class TestSuite(object):
oldtime = self.source_file_mtime
if os.path.exists(self.source_file):
self.source_file_mtime = os.path.getmtime(self.source_file)
- return (self.source_file_mtime != oldtime)
+ return self.source_file_mtime != oldtime
def get_selected(self):
return self.selected
@@ -587,7 +588,7 @@ class TestSuite(object):
return
elif len(suites) > 1:
for xmlSuite in suites:
- if (suites[0].getAttribute("name") == self.name):
+ if suites[0].getAttribute("name") == self.name:
break
else:
xmlSuite = suites[0]
@@ -596,7 +597,7 @@ class TestSuite(object):
xmlCases = xmlSuite.getElementsByTagName("testcase")
for case in xmlCases:
classname = case.getAttribute("classname")
- if (classname == self.classname):
+ if classname == self.classname:
# This is the single test name
test_name = case.getAttribute("name")
test = self.find_test(test_name)
@@ -752,7 +753,7 @@ class TestProject(object):
# This will run while calling the stdout callback.
(status, output) = run_command_with_callback(full_command, callback_func)
- if (status != 0):
+ if status != 0:
msg = "-------- BUILD FAILED! ---------"
if not callback_func is None: callback_func("%s" % msg)
self.build_succeeded = False
@@ -1055,7 +1056,7 @@ class MultipleProjects(object):
word = val[1:]
for pj in self.projects:
for suite in pj.suites:
- suite.selected = not (word in suite.name)
+ suite.selected = not word in suite.name
if suite.selected: num += 1
else:
word = val
@@ -1486,14 +1487,14 @@ def test_results_compiling():
def test_age():
a = TestSingle("my_test_test", None)
- assert (a.state == TestResult.NOT_RUN)
+ assert a.state == TestResult.NOT_RUN
a.age()
- assert (a.state == TestResult.NOT_RUN)
- assert (a.state.old)
+ assert a.state == TestResult.NOT_RUN
+ assert a.state.old
a = TestSingle("my_test_test", None)
a.state = TestResult(TestResult.ALL_PASSED)
a.age()
- assert (a.state.old)
+ assert a.state.old
test_results_compiling()
test_age()
diff --git a/tools/TestViewer/test_tree.py b/tools/TestViewer/test_tree.py
index f373d29ff19abf5b7fb4b5d4189f39e3424d7fb6..9c233db03d27a2f1b4e6569cd9ba148cf84dbf37 100644
--- a/tools/TestViewer/test_tree.py
+++ b/tools/TestViewer/test_tree.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name,no-init
""" An AbstractTreeItem implementation for a QTreeView
that uses the results from test runners. """
@@ -295,7 +296,7 @@ class TestTreeModel(QtCore.QAbstractItemModel):
# What background color?
if role == Qt.BackgroundRole:
- return item.background_color();
+ return item.background_color()
#User role is used when directly querying the contents of the item
if role == Qt.UserRole:
@@ -490,7 +491,7 @@ class TestTreeModel(QtCore.QAbstractItemModel):
for k in xrange(num_tests):
test_indx = self.index(k, 0, suite_indx)
# Sets it as checked.
- self.setData(test_indx, QtCore.Qt.Checked, QtCore.Qt.CheckStateRole);
+ self.setData(test_indx, QtCore.Qt.Checked, QtCore.Qt.CheckStateRole)
def mouseDoubleClickEvent(self):
print "mouseDoubleClickEvent"
@@ -536,7 +537,7 @@ class TreeFilterProxyModel(QSortFilterProxyModel):
return False
if self.selected_only:
if isinstance(item, TestProject) or isinstance(item, TestSuite) :
- return (item.get_selected() > 0)
+ return item.get_selected() > 0
else:
# Don't filter out TestSingles based on selection (since they're all selected)
return True
diff --git a/tools/TestViewer/ui_main_window.py b/tools/TestViewer/ui_main_window.py
index 415f4cf3f0b9fc2ffc51ce79f3bb345c6d99e958..d33d69c8a7d567dd0f6e2337f7b286e84a9f8ab6 100644
--- a/tools/TestViewer/ui_main_window.py
+++ b/tools/TestViewer/ui_main_window.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'main_window.ui'
diff --git a/tools/VTKConverter/VTKConvert.py b/tools/VTKConverter/VTKConvert.py
index 5b84926cc4900576e1ecede9e9337d983153c9a1..3048c2c46f2f3071bb0b9f104c26f61ca1d7706f 100644
--- a/tools/VTKConverter/VTKConvert.py
+++ b/tools/VTKConverter/VTKConvert.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#! /usr/bin/python
# Convert an acor file into VTK format (specifically a vtp file)
from xml.dom import minidom
diff --git a/tools/VTKConverter/processISISData.py b/tools/VTKConverter/processISISData.py
index 7d00849ca3f3d570c99e3dc54354b7cbac107ff3..7a988d0adbbaab4180538af8c941ed45a67dca34 100644
--- a/tools/VTKConverter/processISISData.py
+++ b/tools/VTKConverter/processISISData.py
@@ -1,24 +1,25 @@
+#pylint: disable=invalid-name
#!/usr/bin/python
import os
import sys
import VTKConvert
-if( len(sys.argv) == 1 ):
+if len(sys.argv) == 1 :
print "Usage: processISISData file-name1 file-name2 ...\n processISISDATA dir-name"
exit(1)
names=[]
is_dir = os.path.isdir(sys.argv[1])
-if( is_dir ):
+if is_dir :
names = os.listdir(sys.argv[1])
else:
for i in range(1,len(sys.argv)):
names.append(sys.argv[i])
prefix=""
-if( is_dir ):
+if is_dir :
prefix = sys.argv[1].split('/')[0] + "-VTU/"
- if( os.path.isdir(prefix) ):
+ if os.path.isdir(prefix) :
print "Directory " + prefix + " already exists, please move\n"
exit(1)
else:
@@ -27,7 +28,7 @@ else:
prefix = "./"
for file in names:
- if( is_dir ):
+ if is_dir :
filename = sys.argv[1] + file
VTKConvert.convertToVTU(filename, prefix)
diff --git a/tools/reports/facility-code-changes.py b/tools/reports/facility-code-changes.py
index 2ea10c847d974cb144283e74900c2a675eb52a84..f8f1e906cde51814c8d5fd820b323dceb9f08b5a 100644
--- a/tools/reports/facility-code-changes.py
+++ b/tools/reports/facility-code-changes.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function, unicode_literals)
__author__ = 'Stuart Campbell'
diff --git a/tools/reports/release-list.py b/tools/reports/release-list.py
index f6a48764d64dbeade4b1df4a4ed9dfb7e7a93045..a74995bfa317d57197b2f7726be302e138e8ff08 100644
--- a/tools/reports/release-list.py
+++ b/tools/reports/release-list.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function, unicode_literals)
import csv
diff --git a/tools/scripts/ConvertBadAlgmLinks.py b/tools/scripts/ConvertBadAlgmLinks.py
index 4d7d71e86989bbaa469f1535c5510afdd5ce52ee..6759d9d23b3b5bdf2004bd2afeb048e9b6edd5c4 100644
--- a/tools/scripts/ConvertBadAlgmLinks.py
+++ b/tools/scripts/ConvertBadAlgmLinks.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
import re, glob, os
def grep(patt,lines):
@@ -30,13 +31,13 @@ for filename in files:
#print os.path.basename(filename)[:-4]
with open(filename) as file:
- lines = file.readlines()
- for alg in algs:
- expr = regexs[alg]
- results = grep(expr, lines)
- if results:
- print filename
- print results
+ lines = file.readlines()
+ for alg in algs:
+ expr = regexs[alg]
+ results = grep(expr, lines)
+ if results:
+ print filename
+ print results
diff --git a/tools/scripts/CorrectConceptLinksinAlgPages.py b/tools/scripts/CorrectConceptLinksinAlgPages.py
index 700472f0529451dd752ec48008bf364e34f51806..7dcd787a465a2a84151c64ec152e6b0f2ba720c7 100644
--- a/tools/scripts/CorrectConceptLinksinAlgPages.py
+++ b/tools/scripts/CorrectConceptLinksinAlgPages.py
@@ -1,51 +1,52 @@
+#pylint: disable=invalid-name
import os, re
import urllib2
concepts = ['Algorithm',
-'Analysis_Data_Service',
-'categories',
-'Create_an_IDF',
-'Data_Service',
-'Dynamic_Factory',
-'Error_Propagation',
-'EventWorkspace',
-'Facilities_File',
-'FitConstraint',
-'Framework_Manager',
-'Geometry',
-'Geometry_of_Position',
-'Geometry_of_Shape',
-'HowToDefineGeometricShape',
-'index',
-'Instrument',
-'InstrumentDefinitionFile',
-'InstrumentParameterFile',
-'Instrument_Data_Service',
-'Lattice',
-'LET_Sample_IDF',
-'MatrixWorkspace',
-'MDHistoWorkspace',
-'MDWorkspace',
-'Nexus_file',
-'Plugin',
-'Project',
-'Properties',
-'Properties_File',
-'RAW_File',
-'Run',
-'SANS2D_Sample_IDF',
-'Shared_Pointer',
-'Table_Workspaces',
-'Unit_Factory',
-'UserAlgorithms',
-'Workflow_Algorithm',
-'Workspace',
-'Workspace2D',
-'WorkspaceGroup']
+ 'Analysis_Data_Service',
+ 'categories',
+ 'Create_an_IDF',
+ 'Data_Service',
+ 'Dynamic_Factory',
+ 'Error_Propagation',
+ 'EventWorkspace',
+ 'Facilities_File',
+ 'FitConstraint',
+ 'Framework_Manager',
+ 'Geometry',
+ 'Geometry_of_Position',
+ 'Geometry_of_Shape',
+ 'HowToDefineGeometricShape',
+ 'index',
+ 'Instrument',
+ 'InstrumentDefinitionFile',
+ 'InstrumentParameterFile',
+ 'Instrument_Data_Service',
+ 'Lattice',
+ 'LET_Sample_IDF',
+ 'MatrixWorkspace',
+ 'MDHistoWorkspace',
+ 'MDWorkspace',
+ 'Nexus_file',
+ 'Plugin',
+ 'Project',
+ 'Properties',
+ 'Properties_File',
+ 'RAW_File',
+ 'Run',
+ 'SANS2D_Sample_IDF',
+ 'Shared_Pointer',
+ 'Table_Workspaces',
+ 'Unit_Factory',
+ 'UserAlgorithms',
+ 'Workflow_Algorithm',
+ 'Workspace',
+ 'Workspace2D',
+ 'WorkspaceGroup']
def outputError(alg, algVersion, description, notes=""):
- print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
+ print "%s, %i, %s, %s" % (alg, algVersion, description, notes)
rstdir = r"C:\Mantid\Code\Mantid\docs\source\algorithms"
conceptsPattern = {}
@@ -61,17 +62,17 @@ for alg in algs:
fileFound = False
filename = os.path.join(rstdir,alg + "-v" + str(algVersion) + ".rst")
if os.path.exists(filename):
- algText = ""
- with open (filename, "r") as algRst:
- fileFound = True
- algText = algRst.read()
- for concept in concepts:
- regex = conceptsPattern[concept]
- while (regex.search(algText) != None):
- outputError(alg, algVersion, "found", concept)
- algText = regex.sub(r":ref:`\1 <\2>`",algText)
+ algText = ""
+ with open (filename, "r") as algRst:
+ fileFound = True
+ algText = algRst.read()
+ for concept in concepts:
+ regex = conceptsPattern[concept]
+ while regex.search(algText) != None:
+ outputError(alg, algVersion, "found", concept)
+ algText = regex.sub(r":ref:`\1 <\2>`",algText)
with open (filename, "w") as algRst:
- algRst.write(algText)
+ algRst.write(algText)
if fileFound==False:
outputError(alg, algVersion, "File not found")
diff --git a/tools/scripts/FindIncompleteAlgRSTPages.py b/tools/scripts/FindIncompleteAlgRSTPages.py
index a7573c89ff2705bc520ead33fea9940b662a231f..f4d05d10629102eab5eb160a5ed24eb1b0ff7749 100644
--- a/tools/scripts/FindIncompleteAlgRSTPages.py
+++ b/tools/scripts/FindIncompleteAlgRSTPages.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
import os, re
import urllib2
@@ -6,7 +7,7 @@ def readWebPage(url):
opener = urllib2.build_opener(proxy)
urllib2.install_opener(opener)
aResp =urllib2.urlopen(url)
- web_pg = aResp.read();
+ web_pg = aResp.read()
return web_pg
def ticketExists(alg, ticketHash):
diff --git a/tools/scripts/TestWikiPython.py b/tools/scripts/TestWikiPython.py
index 09ca6e06bc757b869f1ba53f913dd6e33c0c4c7d..63d0e4b367106c17a36bebcbf2cdb8caec1f337b 100644
--- a/tools/scripts/TestWikiPython.py
+++ b/tools/scripts/TestWikiPython.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
###########################################################################################
# Extracts code blocks marked as python from mediawiki pages and checks they run
# run with -h for command line arguments
@@ -133,7 +134,7 @@ parser.add_argument('-o', '--o',
help='Provide a path to output to an output directory')
args = parser.parse_args()
-urlList = [];
+urlList = []
baseUrl = "http://www.mantidproject.org/"
if args.s is not None:
baseUrl = args.s
diff --git a/tools/scripts/extractAlgorithmNames.py b/tools/scripts/extractAlgorithmNames.py
index 90c7a661aed65f9d78fc2fc2878c2f21f3f2b9ea..8945b898c9e698c5c3d261c1d0ba9d35ad42635e 100644
--- a/tools/scripts/extractAlgorithmNames.py
+++ b/tools/scripts/extractAlgorithmNames.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
# simply just print out all algorithm names in a directory which can be piped
# to a file
diff --git a/tools/scripts/extractAuthorNamesFromGit.py b/tools/scripts/extractAuthorNamesFromGit.py
index ee6bf1e2eceb5ff853dc9c5baa93a86814ee91d0..728ac36dadd8f2cc94f81df3cf512a7f4f4b93bb 100644
--- a/tools/scripts/extractAuthorNamesFromGit.py
+++ b/tools/scripts/extractAuthorNamesFromGit.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
# This python script is run after running extractAlgorithmNames.py, where
# the output of that script is saved to a *.txt
#
@@ -18,7 +19,7 @@ allAlgs = [line.strip() for line in open(algorithmList)]
os.chdir('PythonInterface/plugins/algorithms/WorkflowAlgorithms')
for line in allAlgs:
#print line
- fullline = line
+ fullline = line
args = [
'git', 'log',
'--pretty=short',
@@ -30,11 +31,11 @@ for line in allAlgs:
authors = subprocess.check_output(args).replace('"', '').split('\n')
authors = set(authors)
authors = authors - set([''])
-
+
for author in authors:
#print author
fullline = fullline + ", " + author
-
+
print fullline
#line = 'GroupWorkspaces.cpp'
@@ -54,5 +55,5 @@ for line in allAlgs:
#for author in authors:
#print author
# fullline = fullline + ", " + author
-
+
#print fullline
diff --git a/tools/skipped_systemtests.py b/tools/skipped_systemtests.py
index c13d3e140d18102f3e4e847377f2ebcaacca1c8b..3ffdb9fb5837d1c055e93e8f019d11e31384d56e 100755
--- a/tools/skipped_systemtests.py
+++ b/tools/skipped_systemtests.py
@@ -1,3 +1,4 @@
+#pylint: disable=invalid-name
#!/usr/bin/env python
import ast
@@ -33,7 +34,7 @@ def addTestResult(results, case, label):
def printResultCell(mark, length):
- if (mark):
+ if mark:
left = int(length/2)
right = length-left-1
print "%sx%s" % (' '*left, ' '*right),